As stated previously in this thread and many others: It’s a bug pertaining to the flag for the NPC entities whether to acknowledge Freeman by name or not. It will most likely be fixed in a future update. Everyone needs to stop over-analyzing this…
Maybe, but i don’t think it follows the story planned by Marc Laidlaw either way.
the story is that there’s an alien invasion, and during the coverup some dude kills all of them, and they get mad
This was occurring much later than We’ve Got Hostiles. It’s only a few levels later that Shepard is told the marines are pulling out, and a couple of missions after that that we see Freeman jump into the Xen portal.
Yep. Opposing Force, if canon, occurs quite a bit later as a whole than the events of Half-Life in general.
Well, according to Opposing Force, Freeman is kind of famous 
That does beg the question, though - if Freeman fails to show up to work often enough for not-Barney and not-Kleiner to be having a betting pool, how did he win Employee of the Month?
Actually, that scene occurs as the marines are pulling out.
They want Freeman because they suspect he was involved at ground zero, possible sabotage.
Then know it’s him in the HEV because they probably checked the logs, databases and timetables for the Sector C labs, so they know he’s the one that handled the sample.