There would be pretty differing opinions on whether or not you have "destroyed" the live rock or not. It sounds like the process is going to way that you have planned and I wouldn't worry about the black portions.
It seems to me that what you want from live rock is to function as a bacterial filter only.
If the rocks aren't too large, why don't you just boil them? That would do it.
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400 gal reef. Established April, 2007. 3 Sequence Dart, RM12-4 skimmer, 2 x OM4Ways, Yellow Tang, Maroon Clown (pair), Blonde Naso Tang, Vlamingi Tang, Foxface Rabbit, Unicorn Tang, 2 Pakistani Butterflies and a few coral gobies
My Tank: http://www.canreef.com/vbulletin/showthread.php?t=28436
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