I think everyone has made a lot of really good points to answer my question. One thing about the Federation I think we can all agree on is that its pretty ambiguous. Sometimes it's like Starfleet can do whatever it wants, then suddenly their "hands are tied."
I'm not arguing that Lore shouldn't have been disassembled. I'm arguing that he was disassembled without a fair trial. They should have at least done it just to keep their legal code sound. After all, it's not like he would have been found innocent! Even in the face of overwhelming evidence of guilt, a person should still get a trial...even if it is only 10 minutes. The crazy thing was that Data was setting a very bad precedent that might one day have been applied to him.....unilateral disassembly.