Well after killing everyone in the teaser, it's about what she deserved.
Although Janeway did whack her in the past.
A temporal doppleganger arriving at the end is hardly a compromise, unless Janeway was going to kill that Kes too in the original undoctored script.
Kes dying twice would have fit the story better, especially after that rant about how after she went back to Ocampa to live with her friends and family, but they all thought that she was a freak who they were deathly afraid of... But in the end, despite having only weeks left to live, plots a 30 year journey home to be with those same pigignorant racists who fear her because she's a freak.
Kes will always be a poor man's Trance Gemini.