Hell yes. Marquez has shown himself to be a great fighter over the years by his wins and even his losses inside the ring. He may never get a chance to avenge his loss to Pacquiao but he will forever be remembered as the great Mexican champion that gave Pacuquiao his toughest fights (Morales 1 notwithstanding).
If Khaosai Galaxy was on that list (even if he doesnt deserve to be an ATG), why not Juan Manuel Marquez? He is one of Mexico's Triumvirates (along with MAB and EM) he should be in there. Only a moron would think not
If you measure greatness by that standard, very few fighters would be considered ATG. Most ATG fighters have had losses on their record, and that includes one sided losses.
I certainly consider him a first ballot Hall of Famer. And if he is not an ATG, he is certainly on the cusp.