Well, Thomas was chief of the EEOC. I wonder if even one decision ever came out during his tenure that was supportive of a gay person's claim. I'd be surprised if there wasn't. Would that have made Thomas unfit?
Roberts was apparently doing pro bono work for the gay "rights" group, which seems to be a BIG difference in itself.
About the possibility that Thomas might have ruled in favor of a gay party at EEOC -- that's an apples-and-oranges comparison. It is completely possible that a gay might have a valid, factually sustained complaint under federal law. The Supreme Court ruling was a gross misinterpretation of the Constitution -- a terrible example of judicial activism -- and Roberts helped to bring it about.