So, I replayed that mission in my latest playthrough and actually, this time around I didn't find the line that bad?
It comes right after her rather heated argument with Varric, so the threat seemed more like she was taking her frustration out on the Inquisitor rather than Varric? It's actually understandable that she'd prefer to vent at a complete stranger and take out her anger on them, rather than say something harsh to Varric and risk burning any bridges with him? Despite their playful flirting, it's clear that deep down, neither wants to admit that their pseudo-relationship is deeply strained and that they're unhappy with the situation they've been forced into against their will?
Varric even alludes to this right after in Skyhold, that he's pretends things are okay rather than dealing with them? While he says this in relation to how his life has been disrupted post-Kirkwall, the clear subtext and Bianca's chastisement about how he prefers to tell stories of what he "should have done", is that she's probably just as desperate to run off into the sunset with him as he is, but they're simply too afraid to pluck up the nerve to ask?
I dunno if that was the way it was meant, the line is still a tad weird, but it does fit better if you take it as Bianca simply being frustrated about their argument and taking it out on the nearest person in range, which is a rather normal thing that most of us have probably done one time or another?