Grad schools care about:
- Where you went (provides context for performance and level of achievement)
- What you did there
- How well you did it
- What you did out of school (summers)
- GRE/GMAT/Other Test scores
They do NOT care about how you got in. If you go to an Ivy, are active, and do well there (grade-wise), the fact that you got in against a relaxed admissions standard for athletes is not something grad schools care about. I would also mention that the ABSOLUTE MINIMUM academic index for athletes (which they just raised in the last couple of years) excludes 80% or more of high school students, so relaxed admissions standards is relative.
The bigger issue is if an athlete can perform well academically and do meaningful summer activities given the time commitment of being a Division 1 athlete and this is where the relaxed admission standard may have an impact, because grad schools generally won't care that you are an athlete if you have a C average.