Adjust Layout Options--retain object adjustment but lock ruler guides in place

You could capture the positions of all the guides, adjust the layout, and reset the guides via a script. Here’s an example:

//the adjusted width and height
var la = {width:"6in", height:"9in"}

var doc = app.activeDocument;
//save the curent guide locations
var odg = doc.guides.everyItem().location
//setup the desired layout adjustment preferences
doc.adjustLayoutPreferences.properties = {
    allowFontSizeAndLeadingAdjustment:false, 
    allowLockedObjectsToAdjust:true, 
    enableAdjustLayout:true, 
    enableAutoAdjustMargins:true,
    imposeFontSizeRestriction:false}
doc.adjustLayout(la)

//set the guides to their old positions
var ndg = doc.guides.everyItem().getElements()
for (var i = 0; i < ndg.length; i++){
    ndg[i].locked = false;
    ndg[i].location = odg[i]
}; 

Hi Eugene:

Again, I could be misunderstanding, but Adobe uses the word objects to refer to frames (text, graphic and unassigned), and guides to refer to guides. 

~Barb

Perhaps I'm misreading this, but this helpx file seems to indicate this is a feature, not a bug. 

~Barb

—https://helpx.adobe.com/indesign/using/adjust-layout.html

You can lock your guides

And the at the bottom untick the option to adjust locked items