Hi Roym.
As you have mentioned above, you are not able to turn off the option "Open PDF files in web browser" in the Preferences.
Could you please let us know if you are referring to Reader preferences. It would be helpful if you can share the screenshot of the settings you referring to.
To share the screenshot, click on Insert image icon as shown below:

Then click on "Choose File" and browse to the location where you have saved the screenshot.
Select the image file and click on "Open". Then click on "Insert Image" tab at the bottom to add it to forum reply.
If you are trying to disable the Reader plugin in safari, take help of the steps mentioned here: Display PDF in browser Adobe Acrobat, Acrobat Reader
This is to inform you that Adobe Reader 9 is an old and unsupported version.
Also, it is not compatible with Mac OSX 10.11 version.
I would suggest you to use the latest version of Adobe Acrobat Reader DC.
You may install the latest version of the application from here Adobe - Adobe Acrobat Reader DC Distribution
Let us know if you have any questions.
Regards,
Meenakshi