Cards on the table - I don't think Voyager was particulary good, and I couldn't abide Kate Mulgrew/Janeway. However, the Kirsten Beyer books are truly excellent and I really REALLY like them - much more than I liked the show. They are amongst the very best of Treklit.
As you may guess, having no real attachment to the show, any changes don't really upset me at all. I certainly don't miss Janeway and have no real desire to see her return. As I am not alone (the books are selling very well) there may be little impetus to bring her back.
What I will say is that Kirstens work lacks the many flaws that marred the show and even the characters that I didn't like are now rehabilitated. I see no reason that I would not find Janeway to be more sympathetic in Kirstens hands.
If they want to bring her back they will (probably when they want some free publicity) and it'll be O.K. - they don't have to though - Voyager is quite healthy as it is...
I can live with possible flaws but I can't stand the destruction of beloved main characters.
I must admit that when I joined here a few months ago I was quite surprised to find how popular Janeway was (I had never come across anyone with a particular liking for her before) but everyone has different tastes.
I would say that I have some particular favourite characters, and although I would be sad to see them written out, I would certainly not stop reading Treklit if they were. Since the relaunch it is richer and more involving than it ever was whilst the shows were on the air.
Besides which, there is always hope - I am still hoping the Countdown graphic novel is taken into novel continuity so we can have Data back, and I am pretty sure we will see Janeway again at some point...