I might be misremembering, but Gambit didn't even know he was a mutant until he developed his powers. And to be fair, we know so little of him, we don't know if his eyes are a mutation. Sure, many of the guilds probably thought he was a weirdo, but they also likely thought he was the devil, not a mutant. When Gambit was a teen, people still knew little about mutants in general. So, any kind of discrimination he got was not because of him being a mutant.
Heh, considering Bella was yelling Rogue she was a "muttie", she probably never saw Gambit as one.