Its still completely plausible IMO.
He never showed big interest in Klingon cuisine until he met Jadzia. He was raised by his humans, probably with human food. He might not even know that his bowel movements are irregular/unusual, since talking about shit isnt exactly a topic of honor he would discuss with other Klingons. And he always lead a pretty conservative lifestyle, avoiding change whenever possible. Why should he randomly change to a klingon diet?
His mom mentions learning to make Klingon food for him, particularly blood pie. He was probably eating a mix of human and klingon stuff on the Enterprise. Of course, since a good amount of klingon food is served live, his options for good klingon food from the replicator were limited.
Sometimes you just decide to deal with that. I'm lactose intolerant, but I'll be dead in the ground before I stop eating cheese or ice cream. I just don't eat it frequently enough to be a continuous problem.