You can't ever make complete sense of time travel plots. You basically have two logical choices:
- Time is all predetermined - since you already went back in time, you must do everything exactly the same in order for the future to occur.
- Every change to the timeline causes butterflies which in turn spin off an alternate universe.
Trek has avoided the first completely, and the second for the most part. Instead we get "wibbly wobbly" to some degree.
But the fact remains, if the timeline was actually "fixed" already, they would not be back in time trying to un-fuck it, because they'd lack access to the Confederation ship which allowed them to travel back into time.