Gays have been serving in the US military for as long as it has been around, for the most part it has been hidden though.
Will is cause shakeups and make people uncomfortable if it is in the open? For some yes, but this is exactly how it was when the military was integrated racially and when women were mixed in as well. Women still are not allowed in most combat roles but that is partly based on ability with some prejudice mixed in. Very few women are able to accomplish the physical demands of those positions although, I feel if they are able to do the job unassisted it should be allowed.
The only issue I see really is the discrimination in housing. Females are housed separately because of sexual tension. There is no easy fix for this as, if you house homosexuals together separate from hetero, you have the same issues as if you house male and female together. The only equitable solution is that we need to get past these issues and house all, male, female, hetero, homo together. I do not see that happening for a while.
Beyond all of that I have no problems with gays serving openly in the military. If they can do the job, they should be allowed to do the job. Yes some will feel uncomfortable, but that problem is with the intolerant ones, not the gays.