I really don't think this is a big deal. I've had the same MTA card in my wallet for over a year (and a previous one like it for a year before that). I just top it off with $50-60 a month and there's no issue.
I appreciate that this might be bothersome to some tourists, but my experience is that most tourists who buy MTA cards don't calculate exactly how many rides they're going to take in a several day visit to NYC.
I don't think it's a big deal either, but it's harder to argue that it's not a dark pattern at all. I promise you there is a non-zero number of people who are filling up with cash and throwing their cards away when they reach the error "insufficient funds". At least there is some transparency about the fact that those people are really throwing away $1 because the cards themselves unambiguously cost $1.
I appreciate that this might be bothersome to some tourists, but my experience is that most tourists who buy MTA cards don't calculate exactly how many rides they're going to take in a several day visit to NYC.