Yes, they are selling their asses to the highest bidder, however here's my story.
First playthrough. I started as a Loner then I switched to Clear Sky mid game. Throughout my (first) playthrough I maintained neutral relations with the Mercs and I killed only a few of them, only if explicitly being attacked first. Everyone kept telling me that I will eventually get into conflict with them. On YouTube I often see people being happy when they find Mercs to kill.
Anyway I reached the point where I am in a desperate need for Expert Tools. Today I decided to take a guide from Jupiter to Pripyat and then do some walking to Outskirts as I had some quests there along with some yellow good stashes for a chance of Expert Tools.
I stocked up with ammo knowing that I've never been there. Things quickly went South as soon as my guide dropped me in Pripyat. First a Chimera and a Controller. Then Monolith and Sin shooting from all sides. Then some more Giants and Chimeras as I aggroed a whole a Monolith base.
By the time I reached Outskirts I was half empty when all of a sudden I aggroed some other guys, anew faction UNISG which I barely survived, and I was nearly empty and exhausted from all the combat. Didn't know where to go next or even where I was. I just drifted to a building with blue symbols on the map, (store and mechanic) and then I saw a message on the PDA from a random dude telling me that I'm near the Syndicate territory and as long as I behave I'll be welcomed to their camp.
In their camp there were the Mecs. Not only that I found a temporary resting place (without a bed), but I was able to stock up on ammo, repair my armor and get some food and water and some more quests for more stashes. The irony is that I'm still in search for expert tools.
Life sucks in the Zone, keep as many friends as you can.
TL;DR: Everyone kept telling me to kill the Mercs early game for access to cool weapons and armor. I decided to remain neutral with them and today (mid-to-late-game) they saved my ass.