During my years in the Canadian Armed Forces, I never got the sense that less room was made for Francophones than Anglophones. However, I do agree that, to be polite, Quebeckers often start speaking English as soon as an Anglophone says something. The phenomenon is not unique to the forces.
Still, I feel that more could be done to make both French and English speakers more comfortable. I wouldn't go so far as to say the situation caused Francophones to leave the forces or that it hurt recruitment efforts. I never felt that.