Time Baby is fine.

If Time Baby is a chrono-master who rules over time, and is the source of all the future time-traveler's time-travelly-ness... It's improbable to believe it was killed in the series finale.

Perhaps, in that one moment, it was destroyed. However, Bill says himself that he only gains the ability to manipulate time after Time Baby is gone; and Bill's influence never reached beyond the physical time and space of The Weirdmageddon within the borders of Gravity Falls.

So, there's still likely centuries of time wherein Time Baby still exists. Being an all-powerful time-manipulator it's safe to assume that at the moment Time Baby became... Time Baby... It altered time to make it so that it had always existed.

Time Baby always has been and Time Baby always will be.