I'm also annoyed that I can't off the Penitus Oculatus guys hanging around in Dragon Bridge, even after a Stormcloak victory.
I did it once but I think I had to make Maro non-essential with a console command. It didn't seem right to be taking Haafingar for the SCs while also leaving an Imperial intelligence outpost active in the hold.
But I felt bad, because I'd already done the Destroy the DB quest for Maro so he thought of me as a friend. To the point where I got a letter regarding the money he left me in his will approximately 0.0006 seconds after killing him and walking out of the building.
Hmm... I wonder if there's a way to mod the PO banners on the building so they are disabled at a certain point, like when you start the Liberation of Haafingar. I don't think the PO agents ever come out of the building once the DB questline is done, removing the banners would make it seem like they'd withdrawn from the area. If you never went in the building you wouldn't know the difference.
Well, the Imperials don't seem to mind. Interesting....
The Legion and the PO are two completely separate factions that don't intersect at all. Nothing you do with regard to one of them has any bearing on your relationship with the other. It makes no sense, but there it is... necessary I guess to keep people from complaining that joining the Stormcloaks locked them out of the Destroy the DB quest, or that joining the DB locked them out of joining the Legion.