Agreed. If ISU starts to lose faculty and research money, I could see programs and certifications being cut from various colleges within the Uni. This is bad. Very bad. The phrase "I have a degree from ISU" could mean something far, far less in the near future.
You're in the B12. You aren't getting glowing accolades now for academics because of that. Even if ISU ends up in a non-BCS conference it's not going to significantly impact your academics negatively.
In fact, getting into some of the non-BCS conferences would probably actually bolster ISU's academic benefits if anything.