If you're at a base, and there are no Catholic chaplains available, then the Presbyterian chaplain is expected to perform the Catholic mass for his troops, without complaint.
And during a time of war when there is a draft, many chaplains are serving under a Conscientious Objector status. This means that they have agreed to serve as chaplains in exchange for not having to fight. In my personal opinion, a chaplain who refuses to serve the needs of all their constituents should lose their non-combat status, or be charged with dereliction of duty.
While this is a decent compromise, I think it compromises too much.
Chaplains should only be allowed to refuse to perform a wedding if there is another chaplain available to perform it. If a gay wedding is forbidden by their denomination, then they should perform the wedding as a non-denominational service.
There should be no room for "personal objections" on the taxpayer's dime, especially when it comes to serving the needs of those who put themselves in harm's way.