So, I said it was a pudding.
The most recent evidence to Doc being a part of the OSC or at least conscripted to Hargrove to some degree or another is actually more about the O'Malley Imprint.
A brief review.
-Doc is not a simulation trooper (or a normally designated one at least) but a low-level medical officer on loan to the program. (Comments in his introduction and at his return in the beginning of season 8).
-Vic had special information in the file on Blue base that he was not supposed to tell Doc. Yes it could just fall under the integrity of the simulation, but I think the information was about Tex and Alpha, both of whom were not supposed to exist or be in a box canyon in the middle of no where.
-Also, Doc and Vic had to specially tune in to each other at the beginning. Vic was not the same line of command Doc usually communicated with.
-Omega (and all the AI) are more amplifiers of their emotional core in the host than anything else. Doc clearly has some issues if the rage portion of his personality mixed with Church's rage is O'Malley.
-If the above is true than Doc has spent a good amount of energy even before his "infection" in maintaining a pacifist personality when really he seems like the kind of guy who would kill humanity to save the world, he's just so inept (not completely, but I'm getting to that).
-Doc was a wild-card villain in the simulation but Doc/O'Malley together were able to both maintain the simulation and have their own goals.
-He was able to obtain D-batteries: Indicating a wealthy and resourceful benefactor.
-The chain of Omega is he left Tex, went to Caboose, and then Doc. We know that Omega was able to imprint upon Caboose significantly, and as the previous long-term host it serves to reason that Caboose had imprinted upon Omega some too. Take for instance the evil plans from the book. Most of them are ridiculous but the most viable one includes an eco bend and really only falls apart at the end because of a lack of understanding of time-travel. The "intelligent" bits came from Doc.
-Doc has never really been in danger since sidewinder. The most was from the Meta in the wall, but he survived that. He was in SOME danger, can't avoid that, but he also got into that trouble either just being dumb or maintaining his cover in front of Simmons. Remember, being in the wall put him on a path where he could be with MetaMaine and Wash, both of whom were "working for" Hargrove at the time, but likely to betray.
-Doc also (during seasons 6-11) showed up and left right when it was convenient for him and for Hargrove's plans. My biggest point here is when he convinced the Reds and the Blues to help capture the Director he walked off screen (to "grab his grenade launcher") and suddenly the UNSC police show up.
-Also, Doc just went with Donut to Chorus. No "we should report this to command" or "I've been awol for months living with you already," he just jumped on a ship with no complaints. Again I think this is him maintaining a cover to watch the Reds and Blues for Hargrove.
Now the new thing. When fighting against Hargrove, Doc did have some things to say (to maintain his cover) but mostly the O'Malley imprint was talking and taking control. Unsurprisingly but with possibly deeper meaning (as this is a crackpot) O'Malley was the aggressive one about the injustices done by Hargrove. That's Doc's thing, complaining about injustices. It is possible being abandoned by his boss on a planet he sought to destroy has caused Doc some distrust with his employer but there is also the issue of being stuck in a pocket dimension and/or subspace and how he was released from that pocket dimension and/or subspace.
I love Doc as a character, he's well written, and Docnut is adorably wonderful. Something just doesn't settle with me about his character at face value and all of the coincidences. I'll let you all have a heaping bowl of that and eagerly await some of the delicious other dishes I'm hearing about
Omega, plausibly knowing all Tex knows, was likely pissed at the Director as well, but for differing reasons. I still maintain Omega's end goal was to have Tex and any means to get her would be justified. He is rage and not brains. Speaking of which, his previous host was Caboose and the imprintation is there. That's why Omega would have done what we saw him do despite knowing Doc's possible alliance.
Doc can be seen in three ways: dumb and lucky; extremely good at subterfuge; or a unique mix of the two. In these scenarios Doc's active thoughts would have been only on the Reds and Blues and any knowledge of Hargrove and his plots would have been hidden from the direct and open thoughts. Ever notice how Doc was more like his character when the real Omega had him and he almost never shut up? A smokescreen made of part ignorance and part mental slight of hand. Also the AI didn't know exactly everything. Delta was surprised by South's betrayal and York and North felt comfortable having a chat with the AI off assuming they can't recall what the host doesn't actively remember. Church and Carolina both could keep secrets.