One more thing in defense of this: Even back in the days of the original Xbox, Microsoft games appeared on Nintendo platforms (The GBA to be specific).
Back then Microsoft's strategical goal was a different one. It would have been too tall of a task for them to launch their own handheld console to keep Sony at bay with their multimedia push, so they did the next best thing and put games on the GBA and DS to help Nintendo's chances to win (Microsoft's games didn't make any difference, but that was their intent). Of course we know in hindsight that eventually the iPhone and smartphones on the whole buried Sony's ambitions, so there was no point whatsoever for Microsoft to support the 3DS in the same way, because Sony got beat to a bloody pulp anyway.
Minecraft on the New 3DS arrived at a point in time where Microsoft had already decided to start their current strategy of decentralizing their Xbox business. All their games on PC, plus Minecraft on Wii U, New 3DS and later on Switch. Minecraft on Vita and PS4 predated Microsoft's ownership of Minecraft; they could have cut support for those versions, but I suppose they decided against doing that because after the Xbox One disaster under Don Mattrick they were aiming to build goodwill, and pulling Minecraft support for PS consoles would have been a total jackass move to reinforce their image of an evil corporation.
In any case, if nothing else, Microsoft spreading their games to other platforms has made them less hated. If that helps, and if yes, how much, will have to be seen. Xbox One's image was set a long time ago, but we are on the verge of the generational reset where minds are open to view Microsoft in a different light.