They'll be back, for three reasons.
1. They can shape shift, so it is plausible that some could survive the war. Build a colonyship in secret, then full throttle through the dregnin blockade until you run out of fuel, and start again. (it worked for the Aliance in Freelancer...)
2. The dregnin don't kill every last person, it isn't their way to do that (Korath clan excepted for specific in game reasons) although to carry out a revolt similar to the Torians would be orders of magnitude more difficult.
3. It isn't their homeworld which got conquered...