Jason — I do think that a deep front wheel can be a bit more difficult to get used to in crosswinds than a shallower rim, but I don’t necessarily think you need to go all the way down to a box rim. I don’t find a moderately deep rim (up to about 60mm deep, like a Zipp 404) to be all that much different than a box rim. But I’m also pretty short (51cm bike), moderate weight (165 lbs), and have spent a lot of miles on bikes over the years. Your size + the actual wheel design + your comfort level will dictate what you feel best on.
Bottom line — I wouldn’t give up on your aero wheels until you’ve ridden them some in wind and know that they feel much different than your box rimmed version.