Yes, microwaving can kill bacteria. But it is the heat of the microwave, not the microwave's themselves that kill the bacteria.
So most likely, the vast majority of probiotics were not harmed, although some likely were sacrificed, especially any occupying the surface.
However, this sounds like a really cool science experiment. It would be easy to grow harmless bacteria, and then with a control (left on the counter), one in the freezer then microwave, one on the counter and microwave, compare the results. Try it out and post back your results.
As for freezing probiotics. It is very likely that freezing greatly reduces the bacteria, but does not kill off all of it. This study (done by a student who needs to learn how to label his graphs and table better (but I digress...)) suggests that the traditional method of producing kefir is more resilient than commercial products to freezing. http://etd.lsu.edu/docs/available/etd-04252012-155457/unrestricted/obrien-thesis.pdf