Because if an independent wins, the NCR is asked to leave, and have no legal ground to stand on if they want to stay. If the Legion wins, Primm suffers no matter what and fighting to the last man, while a gallant gesture, is totally useless. If House wins then the NCR troops leaving not only have way of fighting back against House with any hope of success, but their leaving might spare the people of Primm any undue hardship. Too bad it's house, who is a textbook fascist bastard and punishes Primm for having the gall of trying to look after itself.