In my life thus far I have had fictional heroes and real life heroes at every stage and Janeway is definately at the top of my fictional pantheon.
Let me just say that I love the character enough that YES I not only read but succumbed to writing fanfiction during the latter years of the TV series and did my first fan-novel nearly 10 years after it ended.
I did the novel because she captured my imagination and I felt there was so much more to delve into with her character, and NOT because some stuffed suit had decided to kill her off. 
Although I appreciate how strongly fans respond to her departure and I grieve with them and wish them well in their crusades, I also see the fear in other fans that this character would be "brought back" after such an ignoble ending. I understand Ms Beyer's (sp?) consternation over Spock's noble Sacrifice in "WOK" being diminished by his resurrection in the following movie and yet I can only say THANK YOU PTB for bringing him back. Without him... the latest Star Trek movie would have paled into insignificance for me.
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I concur all these points. Do you have a link to your work? I'd love to read it. I dabble in fan fiction from time to time, both writing and reading it...but I haven't lately with my day job, night job, and going after my second degree...Guess who's supposed to have page 8 done for a comic book turned in to her editor by tomorrow but is on here instead...

(It'll be done, I only have a panel to go and we all need time to unwind, right?)
I was elated with Spock's return as well. Yes, the same can be said if Janeway returns that perhaps an aspect of her sacrifice will be diminished too, but there is a way that a comeback can serve a purpose that overrides the diminished sacrifice. Besides, in works of fiction, who says heroes must stay dead?