I don't think there's any risk at all. Pragmatically speaking, the number of players who would would actually quit over this crate system being introduced would be replaced within a day of sales. More generally, and for better or worse, the core gaming community has reached the point where it is okay with microtransactions existing in games as long as they are not disruptive to the actual gameplay. The pendulum has swung so far that these days the best we can hope for is that microtransactions don't provide paying customers any advantage over those who don't. Which is true in this particular case. The items available in the crates are cosmetic clothes to wear while you play the game and they provide no benefit to the wearer. I think the game is too popular and the implementation too benign for this to cause any significant damage to the image of the game.
That said, the developer is cognizant of the fact that the news has not been received well in some parts of the community.
He posted an update today explaining it a bit more. The TL

R version is that the microtransaction/crate system was always going to be a part of the final release and the crates they are introducing now are to test the implementation for the full game. And he promises to be better a communicating with and taking feedback from the community going forward. I guess it's up to you to decide whether to believe him or not.