Having to play games with jQuery to strip out or alter some of its functionality just to get it to appease Mozilla really isn't much different than any other bug that might need to be patched to get jQuery to work in a certain situation.
"So I grabbed their code and tried checked if it would also produce warnings, and it did, almost as many as mine."
So, no, not so much. I believe you're confusing this with a statement made after it that does relate to jQuery Mobile.
If jQuery's build system has options to create a version that is compliant with our CSP, I don't see any reason to be up in arms.
As the one person on the list mentioned, the warnings should not be the reason for the rejection because they were kind of false positives, the only problematic thing is that they were.
They are still working out the issues I assume, it is a really young platform yet so it kind of could have been expected. I just wish there was a possibility to talk to the reviewer and ask them more questions.