I would say that yes, freezing would very well likely destroy the probiotic. I recently read a great book on (human) nutrition by Dr. Jonny Bowden which stated that frozen yogurt wasn't really healthful as the probiotics cannot survive freezing. While I know this particular example is a little out of context from your situation, it does seem to suggest that the same would happen with any probiotic.
Understand what youre going through, though. I give my cat Cosequin at every meal, and it always provides an extra challenge... especially since I'm only giving it to one cat and not that other. Good luck!