Yes, If the authorities of Kosovo want to integrate the non Albanian refugees properly they can, and certainly have the knowledge of how to do it. The question is if they will want to or not. They do not care that much about the refugees, or about helping them out.
The American Experiment is a prime example of the adaptability of humans. Cultures that continue to war outside of the borders live in relative harmony in the US. The country is not without racism or xenophobes. Kosovo will have the same issues. The non-Albanian refugees can be integrated if Kosovo makes certain programs available to them, and the refugess themselves can accept that they are susceptible to the new rules of Kosovo.
I do think that non-Albanian refugees can be reintegrated into society by the authorities in Kosovo. It seems to me, from speaking with many people, that Kosovo wants to heal itself. It wants to go through a time of growth, secularization, and really rebuilding. It was hell there for many years, and now it's becoming more kind and accepting.
I don't believe non-Albanian refugees can be reintegrated properly by the authorities of Kosovo. This is because there has been too much ethnic turmoil in the area and even with the help of the government, the masses can still cause problems for these refugees. There would not have been such ethnic issues if the government were able to gain a foothold on it in the first place.
Given that the Albanian population in Kosovo is at about 92% according to Wikipedia, I believe it will be difficult to reintegrate non-Albanian refugees. That's not to say that it shouldn't be done, but it will certainly put a strain on the country and its current inhabitants that are use to being the majority.