You may have to edit a few files to achieve the desired effect, but I'm sure that it is possible. Do you want to globally change the book cover behavior, or do you want to use the ILS-provided images for some records and the standard ISBN versions for others? How do you know where to find the cover images? Are they included in the MARC records or looked up by some identifier? Depending on the answers to those questions, you might need to do some combination of these things, depending on the details:
1.) Add a new field to the Solr index for tracking image URLs.
2.) Edit a couple of template files to change/override the way bookcover.php gets called.
3.) Change bookcover.php to add a new service for retrieving images from your ILS.
I'll be happy to provide more details if you let me know more about what you are trying to do and where you are running into problems.