This seems silly to me. To suggest that Margaret should completely ignore everything that had been established with the DS9 books to bring it into line with the rest of the Trek fiction, because following on with the story in her own manner would upset people doesn't even make sense.
That's not what I'm saying. First off, she didn't "ignore" anything by jumping the chronology forward, any more than TMP "ignored" TOS by taking place several years later. Sometimes an ongoing continuity includes a time jump. It's hardly unprecedented.
And I didn't say it would "upset" people. I said that a creator can do a better job being oneself than trying to emulate someone else. Different creators can be very different from each other, and sometimes trying to stay the course works out badly. Look at
The West Wing. After Aaron Sorkin left, the show floundered for a season. When it tried to stay the course with new people in charge, it just fell apart. It finally recovered somewhat in the sixth and seventh years, but only by making itself over into a very different show, one that better fit the interests and sensibilities and talents of the new people in charge. In a lot of ways, they might've been better off skipping that transitional year and just making a clean break. (And as I recall, they actually did make a time jump of sorts to get into the next presidential election season sooner.)
I also said that it's a nearly universal practice that when a new person takes over as the creative lead of a series, they bring their own distinct approach to that series, and sometimes they do so by making a clean break and starting fresh rather than trying to stay the course. This is hardly the first time in recorded history that that's happened.
Consider this: sometimes a new editor or producer or whatever might simply not
want to tell the story the same way their predecessor did. It happens. You can't do your best work as a creator (or an editor shaping the direction of a series) unless you're doing something that inspires and engages you. The stuff your predecessor was doing might hold no interest for you, or maybe you have ideas of your own that you're eager to explore but that can't work unless you make a clean break with the past. It's about exercising your prerogative as a creator to tell
your stories the way you want to tell them.
My own experience of Marco and Margaret is that they're two very different people with very different approaches and preferences. I don't know Margaret's exact reasons for making the choice she did, but it doesn't surprise me that she chose to go in a very different direction from Marco. Margaret has her own preferences and she's not afraid to assert them.