Yep, it worked out great for both sides.
We likely do not get Flying Colors if Portnoy had stayed in DT, and it is very possible that Neal Morse's solo band does not mushroom into the Neal Morse Band if Portnoy still had DT as a full time gig, so on the strength of those bands alone, it is a major win.
And while business was good for DT at the turn of the decade 11 years ago, the band needed a change, and the best change was the one they got. For all of the good Portnoy did for the band, his iron grip on the band had gotten too tight, and the music was starting to suffer a bit as a result (the last two albums with him were good, but the cracks were showing). The band sounded totally energized again with A Dramatic Turn of Events, which featured some of their best collective songwriting in years, even if I find it a frustrating listen all these years later because of the mix/production. You gotta take the good with the band, and the good has far outweighed the band since the fall of 2010.
So yeah, both sides have come out winners since. And so have the fans.