I pressure cook all of my beans except for lentils (I find they don't seem to save that much time in the PC, but that's just me). As for them destroying proteins, I don't really know about that. I can't really imagine it altering them anymore than straight boiling would, as it's not that much higher of a temperature, and because you're still only using water (as opposed to vegetable oils, coal/some other charring method), I can't really imagine undesirable compounds forming while they cook. I say keep pressure cooking.
Ya Odid, i too think that pressure cooking using minimum water ( not too much) shud not be forming any new compounds, denaturing proteins etc ... Hope so