I don't remember Sisko's absence in the early days of the DS9R to have caused any major ardor for his character's return.
I was too busy enjoying DS9's elaborate tapestry and being thankful to have it back.
Maybe if Janeway had been removed onscreen, like Sisko, and Data were, it would of been easier for non-regular readers to accept.
The problem seems to be, that generally there are two major camps.
Regular Readers who follow the books as a continuing and dynamic universe for their current Trek Fix
and
Non-Regular Readers, who like to remember the shows they loved every once and awhile by picking up an adventure that doesn't deviate too far from the way things were back then their show in question was on the air.
I tend to fall into the Regular Reader camp, and I like the fact that the universe changes and evolves. It keeps things unexpected.
The fact that a character can die and remain dead, that death is significant, and has repercussions... That's major.
The idea that the characters we love can actually be put in danger and we're not sure they'll always get out of it, has merit.