[quote=Wraithblade6]
well, martin's running around is getting a lot of people killed, plus, he's probably going to die. Gettign him captured is at least going to let him stay alive a while longer and spare the death toll.
[/quote]

Getting people killed was his assignment. 

[quote=Wraithblade6]
Hm, you know, that drone has no reason not to blow us both up. Martin probably just took us both out.
[/quote]

Martin gave him a bunch of reasons to not blow him up. Before you impaled Martin.
Anyways, if he does explode immediately he'll take out Martin, Mytias and all the SOLDIER characters who are at base right now. Matt, Lightning, Axel, I bet I'm forgetting a few. He'll take out any chance SOLDIER has of defeating Magnus.

So I bet the robot will either not detonate, or doubt this decision for long enough that martin can get to cover.