I think one of the ways we could combat as well as defederating them from instances is provide such a good user experience to consume content on the fediverse that threads - or whatever else - becomes just a shittier, ad-ridden version of what we use.
Look at Reddit for example, if they didn’t have the power to remove our access to APIs, third party apps would still provide the best experience. Can any of the features Reddit provides that third party apps don’t justify the number of ads thrown in your face? Nope.
Same here, if we focus on improving the experience of a Lemmy or kbin user and ignore whatever meta is doing, nothing is stopping us from becoming just the better way of consuming all fediverse content. Then if threads were to drop federation, we would still have the upper hand.
The only thing that might hurt us in the end is if we start giving in and host communities on their instance. But if we don’t, and keep our ground, we can have the best of both worlds. See their content without their ads, and keep control of our own content, without their rules.