I thought the same thing when I first looked at his Champion. However, although the Argent Crusade's stance is non-segregation and acceptance of all races, the members of the Crusade are still just people. It's entirely possible that there are members of the Crusade who "put up" with the other Faction, or have pre-existing bias. If one of Menthus' superiors had such a bias, and Menthus worked with the Horde, then it would be easy to sully his reputation and make him an outcast in the Crusade through lies or misinformation. It would be Menthus' word against his superior's, and guess who's more likely to be believed.
^ This ^. I probably should have made it more clearer, but the particular superiors he currently falls under, are not very approving of the horde's inclusion in their ranks or activities. They might be tolerated, but to some people, that doesn't mean that they should be 'mixing'.
Menthus has made it a point in his past - even before his time with the Argent Crusade - to work with people regardless of race or faction. If the people were able comrades and pulled their weight, he didn't really care if they were white, green, blue, black or whatever. He doesn't care if they have tusks, horns, tentacles, etc. He judges people for who they are, not what they are. This mindset does not sit well with some folk, including a few who have dominion over him, and as such, he's never been promoted, he's received his fair share of crappy assignments, etc. He's never been outright blatantly threatened or harmed (at least, not yet), so the 'retaliation' is more of a passive punishment for his views.
I hope that helps a bit. :)