I see what you're getting at. When Janeway (the Janeway talking to Tuvok here) said she would have given the same order, she is already admitting she sees the other Janeway's point of view, therefore the "but" and what follows really doesn't make that much sense.
Distilling it down to words that make the lack of sense more obvious:
"I agree with you, but I also see your point of view."
Oh, I see the problem now. Yeah, she's saying that she would've given the same order as the other Janeway, so the "but" when she goes on to reiterate that understanding creates a paradox. "A is true, but A is also true."
So yeah, that is ambiguous. Sorry I didn't catch it earlier. I guess the situation was confusing enough that even the writer lost track.