It used to be that a significant percentage of every class had to be pilot qualified (PQ) to start and thus if you were not PQ, there were less slots available. I wouldn't be surprised if that has changed over the years as the USAFA mission has changed. However, he may find himself limited to an even more narrow set of career fields overall with color blindness.
If you spoke to someone at USAFA admissions and they told you it was ok, you should be fine, but he should investigate USAF career fields and see if he would be happy in the ones that can be filled with someone that is colorblind. FYI - studying aerospace engineering at USAFA is not a guarantee of working as an aerospace engineer in the USAF.