Top Pentagon thinker bemoans “civilian subjugation to the military.”Blistering charges of misplaced power and a morally bankrupt culture in the nation’s “military-industrial complex” are rarely leveled by one of the defense establishment’s own. But that is exactly what an instructor of the military’s rising stars lobbed on Tuesday when he very purposely engaged in friendly fire at a defense budget conference co-hosted by the Cambridge-based Project on Defense Alternatives.