I have to completely agree with everyone else. I think you should have apologized. I don't even see why you would even hesitate.
Sure, breaking down and crying might have been a little over the top, but you also have to wonder what was going through his mind at the time. Was he depressed, suicidal, having one of those days when everything just makes you want to cry? Had people been messing with him about his weight all day, all week, all his life? You can seriously only take so much. And it seems like he was trying to include himself in the conversation, if nothing else.
I love a joke as much as the next person, maybe even more, but when someone is being dead serious about something and is a stranger, it's best not to respond with those funny/rude jokes you'd make with a friend. And are you absolutely sure your friends are even comfortable with it. If I had friends and they were constantly joking about my weight, seriously, I wouldn't count them as friends.
It seriously reminds me of when I'm already upset or angry about something and make a comment about changing it, or fixing it, and someone says something like, 'Yeah, like you'd do it', or 'I'd like to see when that happens', or something along those lines and laugh their heads off, it makes me feel so bad. I wish I wouldn't have said it and had a hole to crawl into. And weight is a touchy subject, and if the guy was being serious about wanting to run and (maybe) try to become healthier, what at all was there to joke about? I don't get that. I feel this is exactly the type of thing that keeps people feeling down about themselves. Even if it was meant in a jest, it can still hurt as much as if you had meant to insult him.