This is an interesting question to think about, though I'm not sure Houseman's poem is particularly analagous to The Great Gatsby. In "To An Athlete Dying Young," Houseman discusses the virtues of dying young, before the accolades of wining the race and the cheers for being the hero of the town are silenced and before the laurel wreath fades and becomes brittle with age. When one dies young, he says, the successes of life are never tarnished.
Gatsby is not particularly young, nor has he accomplished anything particularly noteworthy beyond making a lot of money through shady business deals. When he dies, literally no one mourns his passing. Nick is sad because he understands the hopeless dreamer/romantic had a better heart for love than those who caused his death (Tom and Daisy); however, even Nick has disdain for many things about Gatsby. While the young man being carried through town has done something praiseworthy, Gatsby has not.
The only real point of comparison, then, is that this young man died before he could live out the heartaches of being forgotten and overshadowed by others and so did Gatsby. He only had to live one day with the knowledge that Daisy didn't love him enough before he was killed. To that extent, perhaps he his better off, just like the young athlete, according to Houseman.