Well, that's where I think their plan falls apart a bit. My interpretation was always that they were going to try to stay in the wormhole, effectively removing themselves from the timestream - hence the episode title "Perpetual Infinity". I don't have access to episode transcripts right now, but Memory Alpha seems to support this:

Burnham speculates that perhaps instead of fighting against time, they flow with it, and try to merge the Sphere into the "river of time" itself – sending it so far into the future that it would not be able to harm them. Stamets' examination of the Red Angel's suit has revealed it has almost infinite data storage, which Pike takes to mean that they would input the Sphere archive into the suit, program a destination beyond Gabrielle's anchor point, and let the micro-wormhole take it away forever. "Perpetual infinity", Stamets confirms; Control will not be able to get the data, ever.

However, I think there are multiple ways to interpret the scene, and I think the last couple of episodes of the season are pretty sloppy in that regard.