He's 6 yrs old and probably loves everything you do. Chances are, he won't even notice the colors and if he does, he'll no doubt think it's suppose to be that way. There are many more quilts in his future from Grandma - I'd leave it as is, mentioning it will only draw attention to it.
Consider the possibility that with all that red, it might all bleed together in the wash and all the red squaes could end up the same color - wouldn't that be great.LOL