Maybe. I'm reaching, but I wonder if part of her concern came about due to how Sisko's character evolved. Granted, he wasn't killed off, but his character was taken out of the mix until it was brought back in the DS9 novels. Did Mulgrew think Brooks' character arc would make Janeway expendable and therefore unavailable if the series were to progress to films? It's hard to know, but she clearly had reservations about her character's popularity being dwarfed by Ryan.
I don't think she was as concerned with her own character's popularity per se. Probably she just thought that a) it was uncalled for to throw Kes out (which didn't matter to me since I'm not a big Kes fan) but being on a show with someone for 3 years and then seeing them just get fired could be jarring, especially if they were close. b) I think she cared more about the show's integrity and quality than "her character". When they announced "we are bringing in someone sexy to boost ratings" she probably assumed that they were becoming less concerned with quality and more about ratings. However, Jeri Ryan did bring much needed quality to the show which Kate fully acknowledges in several quotes after the fact. I think she understood after a few episodes that the character and actress had a lot more potential than just 'hot chick'. She admits this many times over the years.