Not really. You have to take into consideration the message being given by the group.
The IKA (official name for the KKK now) website:
Imperial Klans of America International Headquarters
Notice the last paragraph specifically. This group is not tolerant of non-white people at all. It must be assumed that someone who is a member of such a group would also not be tolerant of non-whites.
The military does not allow membership by its members into any group that is connected to criminal activities and/or that advocates intolerance (with or without violence) against others. This would most certainly cause disruptions in morale and good order and discipline. The military insists that all members have tolerance toward all people, no matter race, religion, or sex. This is because all members of the military must work with others in the military of different races, religions, and genders, at one time or another. So how can a military member abide by this rule and still be a member of any group that advocates for intolerance due to any of these traits? It really doesn't work. You can't have trust in someone that you are intolerant of because of a trait that can't be changed, and they certainly are not going to be tolerant of a you if they find out that you don't like them just because of their race, religion, or gender.
Being a homosexual does not make you a member of any "group" that advocates intolerance for any trait, just like just being heterosexual does not, in itself, mean that you a member of a group advocating intolerance for some trait.
Also, this should be obvious, but by "trait", I do not mean the "trait" of intolerance. In order to compare homosexuals to members of the KKK or terrorist organizations, you would have to show how just being homosexual makes a person somehow intolerant of someone else because of that person's race or religion or gender, something along these lines or how they are advocating criminal activity (and sodomy is a) not necessarily practiced by every single person who is homosexual and b) not actually illegal, just against the UCMJ, for now).