Nah it'll be fine. And remember there's a big difference between a system overheating (shutting off due to hitting the TJ max) and a system feeling very hot to the touch. With regards to the latter, Apple use aluminium in their Macs, which displaces heat. So even when it feels hot to the touch, the internal components are actually running much cooler.
In regards of the 2016 15", the cooling system is incredible. It's an engineering marvel. It won't be overheating when under intense stress of running FCPX & driving 2 external monitors, so you can play Minecraft without any concern.
Java sucks, though. So if the fans ramp up, it's not because your computer isn't powerful. It's because Minecraft is far from an optimised game.