There's a .doc FAQ w/ Layne Norton around here somewhere but I can't find the link. Anyways, it reads:
"... proteins are long chains of amino acids that are linked together by peptide bonds. Each protein folds into it's own natural 'conformational' shape depending upon the sequence of the amino acids contained within it. However, [heat] does not 'destroy' the protein, it simply causes it to unfold. The amino acids remain intact and are still available."
So like these other guys have suggested, no, it doesn't destroy the protein and it's fine if you prefer to heat up your sources.