That's my only real issue with her is her comment to the Nova class captain about it.

However, I give her the benefit of the doubt here because she's clearly trying to encourage him that they don't need to abandon their morality. If she tells him that she's done it half a dozen times or so then he might be more likely to assume that's the standard.

Now we all know in hindsight that he'd already committed an atrocity and wanted assurance from Janeway that he wasn't alone in his decisions to prioritize crew over other sapient beings, but she was simply seeing the younger version of herself in him and attempting to assure him that he doesn't have to give up hope and sink to those depths.

Voyager has more of a problem with character writing consistency than it does an issue with Janeway specifically, IMO.