Defederating isn't the threat - the situation you describe would hurt the fediverse, but it would survive as you said.
You're missing the far more insidious piece - changing the standards
So let's say we have mastodon servers, threads, and maybe another player or two.
Context for my example - Lemmy and mastodon use paths, 0.
<root post id>
.
<reply>
.
<reply reply>
.
<etc>
Facebook decides "path isn't good enough for what we want, we're changing the first number, always 0, and we're going to set it to a number from 1 to 100000 that will encode topic, work appropriateness, and sentiment analysis into this value".
Being the majority of the network, suddenly mastodon either throws out the threads content or the clients start breaking - the fix would be simple, but until that happens either they temporarily defederate or apps start crashing.
Either way, people are pissed - either their busy feed has suddenly gone quiet, or their app no longer works. It gets resolved in a few days, and now apps are able to do better sorting
The takeaway for most people is "mastodon sucked for a few days"
Now let's say they use this sentiment analysis more deeply for the algorithm. They've got AI doing it, hell, they're even being "good fediverse citizens" and running it on mastodon posts for free. Everything works better, you find stuff better, nsfw posts are better flagged, the clients add cool new features around it
Now, let's say Facebook decides "mastodon is costing us server time, and we don't make much off them. Let's just show more threads content and only show replies and the top thousand mastodon posts each hour" Suddenly, mastodon users get much less engagement when they post.
Their takeaway is "mastodon isn't as good for us as it used to be"
Maybe someone builds an open source system for mastodon to do classification. It's much more expensive server-wise, so maybe only the top servers do it... But their posts get seen again, and everything is good again. People move to these servers or to threads so they can keep being discovered
Now, let's say someone at Facebook goes "their classification isn't as good as ours, and their nsfw tagging isn't as good. Our advertisers would be pissed if they found out, let's not sell ads on any post not classified by us just to be safe". Someone else comes along and says "we're leaving money on the table here, let's show less of those posts".
And kind of like this, these little decisions made with little malice would slowly choke out mastodon. With a dominant player, the little guys don't need to be targeted - Facebook just has to put themselves first. And if you think a company would consistently pass up on profits or savings for a vague promise as years go by, I don't know what to tell you
If threads is a more stable experience, only privacy minded people would pick mastodon. Even people that refuse to use threads on principle would be less likely to be active on mastodon
In reality, the decisions and side effects would probably be more subtle than this... But it doesn't take much. They just have to occasionally make the fediverse feel buggy or unfinished in comparison, and it'll forever become a place for enthusiasts and never as a serious option by the public at large