Quiting STFs causes a one hour penalty. I wish PvP quitters were punished in a similar fasion. Maybe tie both of them together into a two hour penalty to stop the quitters?
If you leave the STF somewhere in the middle, or towards the end of the instance, you won't get a penalty. I've had to leave STF's multiple times because I get stuck with a bunch of new silver players that don't understand the mechanics of the STF, and won't listen to any advice I try to give them..