Kyrgyzstan is "muslim" in name only. The Kyrgyz are not what you would call orthodox muslim. They drink like fish and party hard.
And they don't like "Russians", or others from the European parts of the old Soviet Union. Understandable from their point of view. The Major, being blue eyed, and fair of skin, may have been mistaken for one of those, at least initially.
Still I'd imagine there are some "more observant" Muslims in the country, particularly out in the hinterlands.