When you run into solder youll have to make a choice and honestly its worth thinking about for a sec. If you take him out permanently you can grab some basic stuff like a broken gun and some ammo, plus a pda with some cryptic message about nestor, but nothing super exciting. The more interesting option though, is just knocking him out - i learned this after a few playthroughs.

Here's why knocking him out is probably your best bet - he shows up later during the hornets' nest mission, and trust me, having him around to disable that nasty psi-emitter makes things way easier. That mission can be pretty rough without the help, especially if youre not great with resource management.

Tip: dont worry too much about faction relationships, cause neither choice affects how others treat you. Solders really just caught up in something bigger than himself, so if youre trying to roleplay it theres some wiggle room there. But from a pure gameplay perspective, keeping him alive definitely pays off later even if you miss out on some quick loot at first