Hmm, never really thought about it before. Several things could be said.
1) Lexaeus is very quiet, "Silent" he preserves his words in most of CoM
2) A hero could be defined as someone who willingly gives of themself without expecting something in return
3) Eleaus, who was Lexaeus' original, may have been the first, or second to enter darkness with Xehanort to see if it was safe
4) Lexaeus sacrificed himself, and blew himself up in an attempt to stop Riku
Yes, he is a villain, but looking at it from the other side, he and the other Org members are trying to help themselves become whole. If someone is trying to stop them from that goal, someone needs to challenge it, right? So, that's my thought on the matter.