Since we don't have a draft but a wholly volunteer armed services no one has to have a reason for not serving -- just don't sign up.
Service persons take an oath to defend and serve their country... Religion does not officially enter into the equation and it probably shouldn't.
I agree that religion should not be considered part of one's service to the USA. Though young men still have to sign up for "Selective Service," there is no forced service at this time. I'm sure there are American Muslims who do not take the extreme anti-American positions that the terrorists have taken and therefore should be allowed to serve their country if they so choose.
I'm Canadian and our young men and women are over there also. If a draft is developed, I think Muslims or any other religious beliefs should be a reason for not serving if one so wishes not to. I can imagine that Muslims in our armed forces MIGHT have a hard time killing other Muslims if they had to. I respect the young soldiers over there, and I support them, but I don't agree with our involvement in the war to begin with. This only my opinion.
There are probably more support functions in the military than combat functions. A person can serve their country, if called upon, or voluntarily, without having to kill anyone. I do not think a person's faith should be used as an excuse to bar them from the military, nor should a person be able to use their faith as an exemption from the military. I do believe people should have the right to refuse to serve in any way in a war they believe is immoral or unethical. There is a big difference between serving to defend our country, and being forced to fight in a war because our politicians don't like another country's politics, or religion, or how they treat their citizens. One man's opinion.
During Obama's campaign, he declared that all youth should serve our country in some capacity for a set amount of time. Youth could work as a volunteer in America or with the armed forces. They would be compensated with a spending stipend and with one year in college or trade school.
I think this would be a viable plan. And, the conscietious objector could opt out of using their volunteer time in the military by simply electing community work instead.
As for fighting those with your own religion or heritage is concerned, being an American gives a person rights as well as responsibilities, deemed by the laws of the land. To remove a certain religious group from serving would be discriminatory.
It is pretty difficult to be accepted as a conscientious objector, but one can apply for it. That is also as it should be; a right.