I get the idea of not letting your damsel-in-distress alone and defenceless in the middle of the wasteland. But when the other party has taken to abduction of acquaintances just to get to you, letting even one escape with their lives seems way too dangerous of a gambit.
Yeah I was thinking this too. While retreating is often actually a great option, this particular group has already proven themselves to be after him in particular, and prefer targeting indirectly through mc's assets, forcing him to accept disadvantageous battles if he doesn't want to simply take the attrition until he's dust.
Add to that how this group knowledge of mc's golden egg, and could screw that up for him if they decide cashing in the intel is better than contesting him for the location. That said, he doesn't know they don't have collaborators in the city that will do so anyway once this team dies. But letting the guy go almost guarantees it.
Besides all that though, with alpha helping him he should really not have issues leaving the girl to jump somewhere high (covering their car) and headshot the dude fleeing. The girl is only in danger if one of those storms appear (which they have some warning for), or the guy gets to his car safely and can use tools there or run her down with the mobility.