Open pdf pages as layers

I would suggest that you use a script such as PDF Processor II where it will open and save separate files one by one, which should be less taxing.

Then use the default File > Scripts > Load files into stack script or a similar script as a second pass to combine the separate files.

It is taxing and will take time but can be automated into a single layer document from all the document opened,

/* ==========================================================
// 2017  John J. McAssey (JJMack) 
// Stack the open Document Visible layer composite into a new 300 DPI document
// This script is supplied as is. It is provided as freeware. 
// The author accepts no liability for any problems arising from its use.
// ======================================================= */
// enable double-clicking from Mac Finder or Windows Explorer
#target photoshop // this command only works in Photoshop CS2 and higher
// bring application forward for double-click events
app.bringToFront();
if (documents.length >= 2) { 
app.togglePalettes(); // toggle off palettes so Photoshop will not need to update them
stackpages();     // Photosho document can be different when oneo via UI
}
else {
var theFile = File.openDialog("Select your PDF file", "Select:*.pdf");  
app.displayDialogs = DialogModes.NO;  
var check = true;  
var page = 1;  
// define pdfopenoptions;  
var pdfOpenOpts = new PDFOpenOptions;  
pdfOpenOpts.antiAlias = true;  
pdfOpenOpts.bitsPerChannel = BitsPerChannelType.EIGHT;  
pdfOpenOpts.cropPage = CropToType.MEDIABOX;  
pdfOpenOpts.mode = OpenDocumentMode.RGB;  
pdfOpenOpts.resolution = 300;  
pdfOpenOpts.suppressWarnings = true;  
pdfOpenOpts.usePageNumber  = true;  
app.togglePalettes(); // toggle off palettes so Photoshop will not need to update them
while (check == true) {  
try {  
pdfOpenOpts.page = page; // open a page at it slower the using Photoshop UI ans selection all the pages you want  
var thePdf = app.open(theFile, pdfOpenOpts);  
page++;  
} 
catch (e) { check =  false };  
}; 
if (documents.length >= 2) { stackpages(); }
else {
app.togglePalettes(); // toggle on palettes
alert("multiple Document are not open in Photoshop");
}
}
///////////////////////////////////////////////////////////////////////////////
//                     stack pages function                                  //
///////////////////////////////////////////////////////////////////////////////
function stackpages() {
var orig_ruler_units = app.preferences.rulerUnits;
var orig_display_dialogs = app.displayDialogs;
app.preferences.rulerUnits = Units.PIXELS; // set the ruler units to PIXELS
app.displayDialogs = DialogModes.NO; // Set Dialogs off
//newFile = theFile.name.substr(0,theFile.name.indexOf(".pdf")); //New File name
newFile = app.activeDocument.name.substr(0,app.activeDocument.name.lastIndexOf("-")); //New File name
var doc = app.documents.add(app.activeDocument.width.value, app.activeDocument.height.value, app.activeDocument.resolution, newFile, NewDocumentMode.RGB, DocumentFill.TRANSPARENT ); // create a new document
//for (var i=0;i<documents.length-1;i++) { // stack a layer for the open document into the new document page 1 on botton
for (var i=documents.length-2;i>-1;i--) { // stack a layer for the open document into the new document page 1 on top
app.activeDocument = documents; // switch active document
var layerName = app.activeDocument.name; // get document name
app.activeDocument.flatten(); // Flatten remove transparency
var idDplc = charIDToTypeID( "Dplc" );
var desc259 = new ActionDescriptor();
var idnull = charIDToTypeID( "null" );
        var ref24 = new ActionReference();
        var idLyr = charIDToTypeID( "Lyr " );
        var idOrdn = charIDToTypeID( "Ordn" );
        var idTrgt = charIDToTypeID( "Trgt" );
        ref24.putEnumerated( idLyr, idOrdn, idTrgt );
desc259.putReference( idnull, ref24 );
var idT = charIDToTypeID( "T   " );
        var ref25 = new ActionReference();
        var idDcmn = charIDToTypeID( "Dcmn" );
        ref25.putName( idDcmn, documents[documents.length-1].name );
desc259.putReference( idT, ref25 );
var idNm = charIDToTypeID( "Nm  " );
desc259.putString( idNm, layerName );
var idVrsn = charIDToTypeID( "Vrsn" );
desc259.putInteger( idVrsn, 5 );
executeAction( idDplc, desc259, DialogModes.NO ); // Copy Layer to document
app.activeDocument = documents[documents.length-1]; // switch to newly created document
layerName = layerName.substr(0,layerName.indexOf(".pdf")); 
app.activeDocument.activeLayer.name=layerName; // label layer with Document name
}
app.activeDocument = documents[documents.length-1]; // switch to newly created document
var layers = activeDocument.layers; // get layers
activeDocument.activeLayer = layers[layers.length-1] // Target Bottom Layer
activeDocument.activeLayer.remove(); // Remove original layer
while  (documents.length>1) { // close all opened document except the newly created document
app.activeDocument = documents[0];
activeDocument.close(SaveOptions.DONOTSAVECHANGES);
}
app.togglePalettes(); // toggle user's palettes back on
app.runMenuItem(charIDToTypeID(("FtOn"))); // fit the document to the screen 
app.displayDialogs = orig_display_dialogs; // Reset display dialogs 
app.preferences.rulerUnits = orig_ruler_units; // reset units to original settings
}
///////////////////////////////////////////////////////////////////////////////
//                stack open pages function                                  //
///////////////////////////////////////////////////////////////////////////////
function stackopenpages() {
var orig_ruler_units = app.preferences.rulerUnits;
var orig_display_dialogs = app.displayDialogs;
app.preferences.rulerUnits = Units.PIXELS; // set the ruler units to PIXELS
app.displayDialogs = DialogModes.NO; // Set Dialogs off
//newFile = theFile.name.substr(0,theFile.name.indexOf(".pdf")); //New File name
newFile = app.activeDocument.name.substr(0,app.activeDocument.name.lastIndexOf("-")); //New File name
var doc = app.documents.add(app.activeDocument.width.value, app.activeDocument.height.value, app.activeDocument.resolution, newFile, NewDocumentMode.RGB, DocumentFill.TRANSPARENT ); // create a new document
for (var i=0;i<documents.length-1;i++) { // stack a layer for the open document into the new document page 1 on botton
//for (var i=documents.length-2;i>-1;i--) { // stack a layer for the open document into the new document page 1 on top
app.activeDocument = documents; // switch active document
var layerName = app.activeDocument.name; // get document name
app.activeDocument.flatten(); // Flatten remove transparency
var idDplc = charIDToTypeID( "Dplc" );
var desc259 = new ActionDescriptor();
var idnull = charIDToTypeID( "null" );
        var ref24 = new ActionReference();
        var idLyr = charIDToTypeID( "Lyr " );
        var idOrdn = charIDToTypeID( "Ordn" );
        var idTrgt = charIDToTypeID( "Trgt" );
        ref24.putEnumerated( idLyr, idOrdn, idTrgt );
desc259.putReference( idnull, ref24 );
var idT = charIDToTypeID( "T   " );
        var ref25 = new ActionReference();
        var idDcmn = charIDToTypeID( "Dcmn" );
        ref25.putName( idDcmn, documents[documents.length-1].name );
desc259.putReference( idT, ref25 );
var idNm = charIDToTypeID( "Nm  " );
desc259.putString( idNm, layerName );
var idVrsn = charIDToTypeID( "Vrsn" );
desc259.putInteger( idVrsn, 5 );
executeAction( idDplc, desc259, DialogModes.NO ); // Copy Layer to document
app.activeDocument = documents[documents.length-1]; // switch to newly created document
layerName = layerName.substr(0,layerName.indexOf(".pdf")); 
app.activeDocument.activeLayer.name=layerName; // label layer with Document name
}
app.activeDocument = documents[documents.length-1]; // switch to newly created document
var layers = activeDocument.layers; // get layers
activeDocument.activeLayer = layers[layers.length-1] // Target Bottom Layer
activeDocument.activeLayer.remove(); // Remove original layer
while  (documents.length>1) { // close all opened document except the newly created document
app.activeDocument = documents[0];
activeDocument.close(SaveOptions.DONOTSAVECHANGES);
}
app.togglePalettes(); // toggle user's palettes back on
app.runMenuItem(charIDToTypeID(("FtOn"))); // fit the document to the screen 
app.displayDialogs = orig_display_dialogs; // Reset display dialogs 
app.preferences.rulerUnits = orig_ruler_units; // reset units to original settings
}