You know, I don't know why I thought that, looking over the scene again, I think she is probably Romulan. There was something that stood out to make me think that but I can't see what it was...
edit: oh it was the 'She's been a useful ally to us for a very long time I can't have her turning on us' in the very next scene with the two Romulans.
I questioned that part too, but then I came to the conclusion that she must have meant an ally within the ranks of the romulan secret cabal . The luitenant fears the commodore turning on them, the them in this context is just the luitenant and her brother not the secret agency.
None of that means the commodore is a romulan or a vulcan, I just dont think we have enough info to go by yet to know how this agency is structured or works.