Alternatively (and somewhat less satisfying): keep the big choice, but have Neelix and Tuvok look aghast at Janeway when they are restored. (After all, they both remember Janeway looking them in the eye and killing them just moments ago.) Add a brief apotheosis in which Janeway experiences grief for her actions. Reveal her to know that she has done something wrong and sense that she has lost something of what she values: she's damaged her relationship with the crew.

This could also be very satisfying. We've established that Janeway is a very moral person and having her sacrifice her morality to get the crew home is a good story. It's "dark" and doesn't fit the tone of the show, but it would at least address the character issue.