You ignore the fact that Marlene tried to take Ellie from Joel because she thought he was going to make the "right choice" by giving back Ellie, but Joel killed her.
There's nothing magical about it. Joel had the upper-hand because he had Ellie. You guys are free to say what would happened if Joel turned the truck back to give up Ellie, but somehow it's impossible for Joel to wait and take people hostage.
Ok, so he is outnumbered, Marlene is in front of him trying to negotiate, with a gun still in her hand. Below him there are at least a dozen pissed off heavily armed fireflies who will be out for blood. Are you honestly saying that Joel stop, tell Marlene to wait however long it is for Ellie to wake up. Aske her if she is ok with dying for a procedure that is no longer possible, and then the Fireflies will just let Joel walk? And let's say that we are wrong and faced with actual death, Ellie says no. Do you think the Fireflies will what, let them walk? When they already proved that her consent is of zero value to them?
You're not thinking this through. I will state it again, from the second that Marlene said "Shoot him if he tries anything." The die was cast. The massacre could have been avoided, but not by Joel. If the fireflies had handled the situation with the slightest bit of human decency maybe Ellie could have convinced Joel. But they didn't. And once they set the events into motion, there was no stopping them.