I'm very sorry to hear that, Saijanta. Forgive me if I say, though, that I do not understand how it feels for a person to simply dump someone because I've always found us humans to be predictable (unless they're online) and have also experienced a few "best friend's betrayal" in the past which I managed to forget. Thus I never take people's words for granted, no matter how much they mean (which is why I don't have many "true friends"). I don't want to sadden you so I'll try my best to appeal to your professional nature instead instead of your social one.
You see, human relationship sort of fluctuates in time, sometimes being closest while at times being at the brink of tearing. Yes, even with the closest of relatives or friends. At the same time, all a human being needs is love; a place where he's adored the most he'd wag his tail right there, loyal to his communities until he finds a better place -- like a mix of cat and dog. We seek community and some of us are usually willing change our beliefs just to blend in with the crowd, and when needed, protect the community no matter how wrong they are. Basically, protecting friends. And like FaustWolf mentions, his sudden lack of interest towards one friend/community and going for another certainly brings his loyalty into question.
Of course, what he did say was indeed hurtful, but I do have something to add. Considering you're an atheist, from your point of view worshiping a non-existent being would indeed be primitive, but for those who believe think that loving God would make miracles happen. I beg to differ, because if there's a reason why God created us would not be to bless us; if one truly believes in God and knows how a superior mind would work, staying lazy and praying for things to happen would make even God facepalm. No, Gods have little to do with miracles and judgement. If God exists, he's there to watch his creation burning with the flames of passion and dreams, stepping through obstruction towards the light, facing the darkness with a candle and burning the grounds so to let there be light.
You may be ill, Saijanta, but you're one of the strongest I know. You take arms against oppression towards helpless people, you take up a pledge to protect your friends. And I dare say that if a God exists to influence fate in any way, he would be a complete asshole to hurt you in any way.
I don't know how I could console you as I'm not good with words, but I hope for the best. Godspeed and may you live to your fullest and blessed.