It is, as you say, an episode that puts Janeway in a no-win situation. And the thing is, she knew it. Look at her face at the end of the episode. She's not clapping Tuvok & Neelix on the back and smiling broadly at their return. She says a curt, "Glad to have you back" and walks into the hall where she pauses with a look that says the entire weight of the universe is on her shoulders.
She isn't happy with what she just had to do. She will, however, live with it.
I, too, liked how that last bit was played. However, I always thought the issue warranted a somewhat more extensive discussion. Or a discussion at all
. The way it is presented – with no-one from the crew, not counting the Doctor, supporting Tuvix heart-breaking pleading to let him live – makes the crew look very cruel. One moment they act like Tuvix' friends, the next they assist in his murder.
I would have been nice, if they had presented some kind of coda to the episode. Just a little scene right after (or before) the execution on sickbay, where Janeway gets the chance to voice some sort of ambivalence about the thing she has just done. The way it is shown makes it look like a much too easy decision for her.