That's completely over-simplifying it. It wasn't just a random joke or something he made. He went on multiple massive twitter rants basically troutting on all people of color and how white people are soooo victimized. Yes, he is of Middle Eastern descent so I'm not sure where this is coming from. And yes, he can still be racist against people of other ethnicities regardless of whether or not he himself is a person of color/is of POC descent.

As for the whole Yooka-Laylee stuff, this is the first I've heard of it (even the bit about him being involved with the game!) but a company is well within their rights to remove a collaborator that does not align with the company's values, especially when that collaborator is giving them negative press.

They probably aren't handling it well. They should have made their definitive statement about JonTron not representing the views of the company, why he was being removed from the game, and then not replied in any way (including not deleting comments). For good PR purposes, they probably should give refunds/returns to those who don't want the game now--as long as the person who wants a refund no longer has access to the game.

tl;dr They could be handling it better from a PR point of view, but they made the right decision. A decision that they are well within their legal rights to do.