I just finished a full viewing of the 2D blu-ray. The tint isn't really noticeable at all.
I think the more naturalistic color timing in the 3D version has something to do with making for a more comfortable stereoscopic experience.
The fact that there are differences like that lens flare is a pretty clear sign that we're dealing with two distinct cuts of the film.
As such, I would imagine the 2D color timing is exactly how Gunn wanted the final film and isn't a mistake.