That was my only real problem with the film as well. Especially after the court room sequence where Bond trusts her by tossing the gun over to her. It just doesn't seem like she'd be one to go to the desk after that sequence.
Unless the producers are playing a long game with this version of Moneypenny. I just get the impression that she'll get from behind that desk to help Bond in one of the next two pictures. Just a gut feeling.
Bond clearly didn't want her in the field (all his hints), but that doesn't mean he doesn't want another person on his side in a firefight if she's standing right there. I think that some people wouldn't psychologically want a job where they might accidentally murder their coworkers. I had no problem believing Eve had had enough of that lifestyle by the end of the film. In interviews Harris said of Moneypenny that "she thought she was Bond's equal, but she's not."
She's a good asset but one that probably can do more good behind a desk, leaving murder and death to the men, like Bond, who live for it.