I think that the degree and breadth of unhappiness that her use in Before Dishonor produced suggest that she was misused, whatever the dramatic arguments to the contrary.
So wait, what you're saying is that some people bitching on the internet make a perfectly valid portrayal of a character a "misuse" of the character?

I totally agree with rfmcdpei, Janeway's behavior in BD was perfectly in line with her portrayal in the past, only that this time her attitude comes back to bite her in the ass.