So keeping Janeway relevant and interesting would have been a "challenge"? Why couldn't Janeway have changed her mind about going back to delta and decided to be the Fleet Admiral? Sisko couldn't have gone back to work without going through a divorce. The stories are compelling and interesting as is. However, I think out is silly to say these characters can't have amazing stories and careers while either having happy family lives or desk jobs.
For example, take Clive Cussler's protagonist Dirk Pitt. Most of those books had him in a job that put him in the center of the action while meeting new loves and occasionally watching them die. Now Pitt is married with kids and a government desk job. However, he still leaves his desk in assignments and has adventures just as good as in Cussler's earlier works. A desk and a family is not the death of a character's ability to be compelling, have adventures, and generate emotion from readers. Cussler and Pitt have proved that.
The books have been great and I in no way wish to undermine their value. But the direction the franchise went isn't necessarily the best way, it is just the way that was chosen. it is what it is. In life there are times where we zigged where we could have zagged. No matter how great our life is, who's to say it couldn't be better or equally as good if we didn't take a different turn in the fork. Take the hand your dealt and make the best you can with it, but don't think you couldn't have had a better hand to work with. Most of the time that isn't true.