That is a completely valid take here. My partner who runs our Mastodon instance will be preemptively defederating with Threads (on my suggestion), so I do agree with you, but I realize not everyone in the Fediverse may share that take - it's a weighted scale where one end is "mass adoption of a Web 3.0 decentralized Fediverse" and the other end is "but adoption in which most people are on Threads will be centralization anyway, so we will have already failed."
I think in any case it may not matter, as I believe Meta / Threads will only federate with instances that agree to follow their moderation standards - after all, Meta likely doesn't want porn and Nazis federated to their communities because then they can't run advertisements. As a Fediverse community, we're pretty good at taking care of the Nazi thing, but Mastodon's got an awful lot of porn on it.
It will really depend on which admins take that deal to be beholden to Meta's standards, potentially opening themselves up not only to huge moderation concerns but to a future requirement of taking advertisements. I hope large instances will not. I would prefer to see the Fediverse operate separate from Threads, who will be using the ActivityPub protocol but not part of the larger Fediverse. Similar to how the conservative "truth.social" uses the Mastodon application and ActivityPub but is not part of the Fediverse because it is closed off.
A little off topic, but I was very surprised Reddit didn't pursue a similar approach of "we will lower greatly the costs of API but we will serve advertisements in the API as regular posts, so you must display them and can't strip them out."