Starsector 0.97a is out! (02/02/24); New blog post: Simulator Enhancements (03/13/24)
I haven't been able to use the ability due to it not being added to old saves so I'll say I'm kinda shocked to hear that you can't deactivate, especially since it can affect allied fleets as well! Seems like it is defs something you should be able to cancel during it's charge time.
However, letting it be abortable will make it slightly more powerful; as it is now you have to commit to standing still for a few seconds.