All of my previous playthroughs of SoC involved helping Duty. This time I worked for Freedom, and as expected, Duty now considers me an enemy.

This makes the Rostok/Bar area a bit of a problem. They attack me on sight, and they man all of the paths leading into and out of the area. If I fight back, the loners then also become hostile to me, as do 2 of the guards in the Bar.

If I run past the checkpoints, I usually take some damage, but Duty won't follow me, and all is good until I try to leave again.

This area is central and I find myself frequently passing through it. Any way to make this easier? Such as a way to sneak around the checkpoints or bribe Duty into becoming neutral?

Aside from arming up and preparing to fight like mad, I can only suggest the no fences minimod

I didn't notice this before, but there's a path from army warehouses to Yantar, and another from Yantar to Agroprom. This lets you bypass the Rostok area entirely. I can't remember if these were in the original game, or if they were added by the ZRP mod I installed. Those paths are a bit strange, because other than on the map, you can't really tell there's an exit there since it's blocked by a barbed wire fence. I was only able to trigger the exit by jumping into (over?) the fence.

I also just got fed up with duty and eradicated them from Rostok. Oddly enough, while I was purging their base, the accusations of "murderer" from the PA system stopped. After this, none of the neutral stalkers or the 2 guards in the Bar bothered me. There was only a handful of duty-loyal stalkers in the NW building that gave their lives in vain to stick up for those fascists.

So now I have a duty-free zone, so to speak, haha.

One other problem that came up was Sakharov was foolish enough to hire some duty goons to guard the bunker in Yantar. After disposing of their bodies, old Sak and his assistant turned into enemies on me. I had to lure Semenov outside and put him down, but Sak still deals with me, despite his status. Guess he knows who's boss, huh? Mind you, his prices now reflect his attitude..

yeah, those level connections are modded in.
if you do a fresh start (and have the opportinity to join a faction from the start in that mod) then try playing the whole game as a Monolithian - extremely challenging until the end - very weird too.