To summarize, average GPA at Williams has risen to just shy of 3.6, and in upper level courses it's more like 3.7. So these kinds of academic honors come with an asterisk attached. Probably the same at other similar schools - at Harvard average GPA is 3.7.
Williams definitely lowers it's academic standards for top athletes more than schools like Bowdoin (same conference) but less than the Ivy's would. The real lesson is that all these schools are much harder to get in to than they are to do well at, so the athletes that get a huge boost in admissions can still do well in school and come out with a good education. It's just a question of admission priorities. I believe every year the Williams T&F/XC program gets 1-2 "slots", which are a really big boost in admissions, and a few "tips" which can basically break ties but won't get a subpar applicant in. That is probably why they have had so many great runners but have struggled with depth for XC.