Maybe Scully would have had better luck trying to reach Mulder regarding Diana if she hadn't gotten erratic about it in front of the Gunmen. Mulder likely felt embarrassed and the Gunmen looked entirely nervous, like children watching their parents argue.
Mulder also likely carried some bitterness from the early season when Scully humiliated him in front of the committee after Fight the Future events. And now it happens again but with an audience whose opinion Mulder actually cares about.
I definitely think that that argument (and a lot of their growing tension (negative) through season six) is a direct result of Scully refusing to say "Aliens" at the hearing. In a very real way that refusal lost them the x files, but I think Mulder could've forgiven that if he didn't feel like she was lying to herself about it. I've talked about this before, but the fact that CC put such a strong restriction on both of their abilities to grow or mature in any way that could change the Believer-Skeptic dynamic, outside of just swapping for an episode, means that as the mytharc gets more complex, Scully appears less and less rational. And at the beginning of season six when, despite all of the actual scientific evidence that she witnessed and gathered that indicated at the very least that there existed a previously unknown parasite that killed human hosts, she testifies that it can't be aliens on the basis that the virus has recognizable proteins. This is despite the fact that the whole Gibson Praise thing had her concluding that everyone has dormant ancestral DNA which could be alien in nature (her dismissal also ignores the fact that there's no reason to believe alien life couldn't form out of the same proteins that were successful here, unlike hypothetical unknown alternatives we know those ones work). So I think on that particular grievance, given their ongoing emphasis on mutual trust, respect, and dedication to the cause, Mulder feels like Scully betrayed him and their work by ignoring evidence to avoid an uncomfortable truth, particularly as her conclusion requires her to completely discount his entire eyewitness experience (seeing as she offers No alternative explanation for why he saw what he thought he saw) rather than simply disagreeing with his conclusion as she normally does. And I think the longer they're not on the x files his resentment builds, even as he's trying to get their place back, and Diana is there telling him she believes him and she's trying to find the truth too while he's being barred from the search, which is exactly what he wants to hear. And Mulder, despite what he might like to believe, is quick to trust and easy to trick as a result. He's clearly experiencing some pretty significant depression during their absence from the files and is even more desperate to latch onto anything that gives him hope for his quest, and Diana is oh so willing to provide just that.
As to the Lone Gunmen, I hadn't considered how their part in that fight might've influenced Mulder's decision to lash out that way, but I think you're right. Specifically, I think it creates yet another breach in their trust when she asks them to look into Diana. By One Son Mulder has become increasingly agitated and paranoid, and Scully conspiring with the Gunmen to go behind his back to investigate one of the only other people on his trust list feels like betrayal from multiple fronts and he goes on the defensive as a result. And given the way that he immediately goes to check and see if Diana really is sketch, it's not that he doesn't care about their concerns, but in the moment especially, he cared more about the implication that his judgement was questionable than his actual attachment to Diana's trustworthiness. And maybe that's another reason he went with the "personal" accusation, because if Scully's motivation was jealousy, then Mulder's professional assessment of the situation wasn't under fire. Which would be one hell of a deflection, especially because for them, the professional is and has been personal the whole time.
Thank you for bringing up this new layer to that fight that I totally forgot about :)
