2 things can be true at once.
Haymitch is a wonderful boyfriend who genuinely loves and cares about Lenore Dove. He would risk his own life to keep her safe without hesitation (which he demonstrates several times), and heās overall a wonderfully considerate boyfriend who cares about Lenore Doveās interests and validates her emotions, even when he doesn't understand them or he finds them difficult. He is a great romantic partner to Lenore Dove.
Clerk Carmine is 100% justified in being suspicious of Haymitch, his intentions with Lenore Dove, and the potential danger he could pose to Lenore Dove's safety.
Remember everything that Clerk Carmine has experienced over the course of TBOSAS; Haymitchās father was a well-known rebel, and the for the Covey, involvement with rebels has only ever led to their deaths. Clerk Carmine's older brother, Billy Taupe, was shot and killed along with his girlfriend Mayfair due to his involvement in a rebel plot. It's unclear whether or not Clerk Carmine knew that Lucy Gray was also implicated due to her accidental involvement in said plot, but what he does know is that she went into the woods with her Peacekeeper lover, and disappeared soon afterwards. It's also heavily rumored that Lenore Dove's mystery father was related to the Chance family, who were also well-known rebels, so assuming that Maude Ivory is indeed Lenore Dove's mother, and assuming those rumors hold some weight to them, that means that Maude Ivory was another Covey member who died because of her romantic involvement with rebels. We could even go so far as to point out that Clerk Carmine keeps his relationship a secret because he knows that queer people in Twelve are arrested and harassed by Peacekeepers, and so Barb Azure's absence from Sunrise on the Reaping might have been a result of her being targeted by Peacekeepers due to her relationship with another woman.
Because of all of these combined experiences, he knows all too well that if the Covey doesn't stay on the good side of the Peacekeepers of Twelve, then they risk losing more of their own already limited members. And in each of those described instances, it's the Covey members romantic partners that lead to their ultimate demise/disappearance. So no, it's not at all unreasonable for Clerk Carmine to get suspicious and/or worried when he sees Lenore Dove dating a guy who is not only the son of a rebel, but also a part of an illegal moonshine business.
Villainizing Clerk Carmine for his understandable distrust of Haymitch is an incredibly shallow take on the situation at hand. Villainizing Haymitch because of Clerk Carmine's distrust of him is a gross misreading of his relationship with Lenore Dove. At the end of the day, both of them are people who care about Lenore Dove a lot and just want the best for her, and that's precisely what makes their dynamic so interesting.