All else being equal, it logically makes sense that 7.62x39 AR15 bolts would be weaker than their 5.56x45 counterparts. That said, I have not heard such chatter since 7.62x39 AR15's became popular. I don't know of anyone performing a torture test. Even if they are weaker, is it really that much of an issue if one breaks? 7.62x39 AR15 bolts are cheap. Not that I'm suggesting one for actual duty use, but I have no issues running my M16 with a 7.62x39 upper half.

Regarding the CMMG MK47 not playing nice with some AK47 magazines, I think that a rifle that's supposed to take AK47 magazines that won't run with actual military grade AK47 magazines is a failure. In my opinion, it's less desirable than having to use 7.62x39 AR15 magazines in a 7.62x39 chambered AR15.