Re-signing Millsap in 2013 means we don't draft Exum in 2014. As great as Millsap is & as much of a question mark as Exum still is (even more so now that he is coming off of an injury), Millsap's presence is unlikely to propel this team to title contention (although re-signing him likely changes our current roster structure so it's impossible to definitively say that) while Exum reaching his ceiling still makes that a possibility.
Not only is Exum a better fit with our core due to his age & position, re-signing Millsap likely doesn't alter Kanter's fate with the team (although it may have sped it up which in return might have allowed us to recoup more value in return). It also could have potentially disrupted/delayed Gobert's development as well as caused us to miss out/pass up on drafting Lyles in 2015.
As hard as it is to watch this team miss out on the playoffs by a single game while a fan favorite excells, I believe the team made the right decision in the long run. Ultimately, Exum & Lyles (+ GSW's 2017 1st rd pick) along with Burks, Hood (who could've still been the selection in 2014 without the GSW trade), Hayward, Favors, & Gobert gives us a better chance at a future championship than Millsap (+ whoever is drafted in place of Lyles) does.