Personally, I have a very poor opinion of nutomic. And yes, he has always been/felt transphobic. He has a history of making massive oversteps to attack people that have differing opinions to his, and overall I believe him to be a threat to the trans community. As for whether we should defederate? I really have no clue. It certainly isn't a bastion for blatant transphobia, and hosts many of the top Lemmy communities, and a very large amount of the active Lemmy userbase. I think the effects of defederation would be immense, and take a lot of time and consideration to understand if it's overall beneficial to the community. That being said, I'm sure I could be swayed to support either side. I'd be very curious what Ada has to say about this, as I believe I'll support her opinion on the matter.
EDIT: I think it's valuable to point out that any individual user can block an instance in their settings. So regardless of any defederation decision (which Ada seems opposed to), anyone can choose to block the instance themselves.
I mean, the two big communities for me are !linux@lemmy.ml and !mechanicalkeyboards@lemmy.ml, though the latter of which isn't really active anyway so I wouldn't be sad to see it go. There isn't a suitable replacement for the Linux community elsewhere, and that's honestly what I'm most active on, but if we defeferate, I'd probably just cut my losses. Yes, it is easy for people to create new accounts, but the hassle is that you cannot transfer your comments or posts to a new account, so you lose that history (as I've had to deal with). But overall, I think most people on ml would just stop seeing posts from our instance and never think about it. It would be a small minority that would even notice, but the majority would be getting less content from diverse voices in the queer community overall. Again, it would just take a lot of consideration.