Had the same problem just yet. Solved it as follows:
- Resetted the quest
- killed everyone
- tried to access bridge via locked door
- deactivated ALPHA first, then BETA, then GAMMA (obvious path would be heading for the two on the west side first)
- killed Angral & Kira
- escaped the fastest way possible
- entered my ship, used the holoterminal, headed for tython and... voilá
- questtracker didn't send me out of the Jedi-Temple, but straightforward to Jedi-council chambers