Brody was never pardoned so much as he was given an ultimatum: Work for the CIA or be sent to Gitmo for the rest of your days. It was the same sort of deal Javadi got after killing his ex-wife.
As far as the truth ever getting out, I'm sure Saul has considered the possibility, but I think he also realizes his days with the CIA are numbered. He has one last chance to accomplish what he's been working towards for decades, so he's put all his chips in. Also, I don't think he sees Brody's innocence as much of a liability. Of the few people that are convinced of his innocence, what proof do that have? Javadi's word? What good is that? The only person who would be likely to argue that the CIA killed an "innocent" man would be Carrie and, well, her credibility has been pretty much shot to hell already. Saul thinks ahead. I don't think he would've done something so risky as employ the most wanted man in America unless he knew he had some insurance - not just for himself, but also for the agency.