People assume that since Serbs are nominally Christian (even though less than 10% of the population are practicing Christians) and since Kosovo Albanians are nominally Muslim (even though less than 20% of the population bothers to attend mosque services and most Kosovars are alcohol-drinking secularists) that this is the religious equivalent of backing Iran in a war against Ireland.
Both groups are largely post-Communist secularists.
What it comes down to is: should the US neuter NATO and go against the EU here? Will Russia really be gratified and begin a more constructive relationship if we do that? Of course not.
Russia would be gratified if every single Serb was slaughtered by Albanian nationalists as long as the USA agreed to dismantle NATO.
US foreign policy general tries to accomplish good while furthering US interests: this move does the good of avoiding an otherwise-inevitable bloody separation while furthering the US interest in preserving NATO's integrity.
As an aside, I have an acquaintance that has gone to Croatia as an evangelist. From what I gather they have lovely, empty churches that they are very proud of, in the same way we are proud of a historic monument. He says it was one of the least evangelized areas in the world.