SOFIA is (of course) an infrared instrument. For infrared, water vapor really messes up the light, like trying to see through fog. So getting above almost all of the water made up for the complexity added by a moving platform.

If a glider could get up there at a pre-determined time, and fly a stable course, that would be really cool. If the glider can't be relied upon to be on-station at a certain time, perhaps because of sensitivity to weather on the way up, then it would be hard to plan your science.

Someone should try it!