Turkey coup

As I watch the attempted coup in Turkey unfold, I find myself being drawn into a conspiracy theory and that is something I try to avoid. It is causing me to impute motives and that is usually a mistake. The conspiracy is that Obama is a Muslim at heart and the motive is that he wants to help Muslims. When the Muslim Brotherhood was elected in a free and open election and later overthrown by the military, Obama sided with the Brotherhood stating that they represent the elected government and the US should stick by them. Now in Turkey, Obama is once again siding with the Islamist Erdogan against the military. If Obama is truly against these military people for the reasons he states then that is perfectly legitimate but I find seeds of doubt entering my thoughts and therein is the concern I have about my thinking. When Hamas gained power in Gaza by way of free and open elections the US not only did not back the new government but tried to remove Hamas. At that time the US pushed for secular governments and worked to prevent Islamic governments regardless of election results. The US concern over the shortcomings of Shari Law was strong enough to fight openly against governments that might want to install Shari Law. The question arises, is it ever OK to disregard the will of the people if what the people want is harmful to part of the population, in these cases the female part?