Jon Snow was 10000% right when he allowed the remaining Karstarks and Umbers to keep their lands. He was right because if he followed the idiotic demands thrown at him to strip those children from their lands, he would have created more enemies for himself and the Starks. Allowing the innocent children of dead traitors to keep their homes wasn’t just the morally right thing to do, it was the best political decision. If he had stripped them of Karhold and Last Hearth, he would have risked alienating the people who are still loyal to House Umber and House Karstark. Whoever he gave those lands to wouldn’t be able to hold those lands peacefully since there would likely be uprisings and minor, meaningless wars that would only continue to weaken the North as a whole and distract Jon from the true enemy. Also, keep in mind, there was just a massive civil war last season. It isn’t as though the Starks have an endless supply of soldiers to enforce the new rule of whoever the idiots want to gift those two subregions to. By allowing the remaining Karstark and Umber to return to the fold, Jon showed his people that he wasn’t an irrational fool driven by vengeance over logic, gave those two Houses and their supporters a reason to be loyal to him, and helped him peacefully unify the North without wasting more lives and time on political upheavals.
Even the ruthless Tywin Lannister understood this.
“Joffrey, when your enemies defy you, you must serve them steel and fire. When they go to their knees, however, you must help them back to their feet. Elsewise no man will ever bend the knee to you.” – ASOS
TL; DR: Jon was right and has begun to redeem himself after the personality transplant of S6.