The only instance that I'll usually immediately give a side-eye to is Hexbear, and only them because a significant percentage of those folks have a certain.... style and culture that gets on my nerves. But an individual can still be a cool person and it's not like I'm about to come in the comments and dunk on you or preemptively block you based on your home instance. I block users because they're assholes, or annoying, or argue in bad faith, not based on where their account is hosted. And I would expect that's probably consistent across most lemmings. You won't get a bad rap only for being affiliated with ml. Now if you say something stupid somebody might use it as a bludgeon to talk bad about ml as a whole, or vice versa, but that's going to happen any time you have something approaching "team sports" like this.
In general, don't stress this too much. In specific, keep up with what's happening on your home instance and if they're doing something you don't like, pack up and move elsewhere. That's a core function of the way the fediverse is constructed. If it sucks, hit the bricks. You can just leave, and set up shop in another instance, or host your own, and you aren't beholden to anyone. But if you don't care then you don't have to.
This is why I threw in with the Star Trek fans. I'm only moderately familiar with Trek but I know these nerds will be nice to everyone.