Yeah, it feels rather short sighted of Andor to make two somewhat contradictory decisions:
1) Follow his professional ethics and kill the traitor so that he can complete the job he was paid for.
2) Burn bridges with his employer and go on the run using his own limited resources.
I guess Andor is still thinking the work is too risky and just trying to stay alive, but he's already in deep. But maybe he's just burning the bridge with Vel, knowing that she's never going to trust him after he killed Skeen and this is the only safe way to exit the situation.
On the other hand, he has no way of reconnecting with Luthen without Vel. So maybe he has to go back to Bix to get reconnected.