(edit: after reading some other threads on TimeWarp.SetRate related issues, recompiling alone might have worked as well.)
An actual fix.
In FlightComputer.cs line 284:
I changed
TimeWarp.SetRate(TimeWarp.CurrentRateIndex - 1, true);
to
TimeWarp.SetRate(TimeWarp.CurrentRateIndex - 1, true, true);
and recompiled. I've tested it and I can take off again, so it seems to have done the trick.