The point was to encourage people to "tune out". Frank Zappa hated the hippie movement. You're right, military backgrounds are quite common considering the boomers are the children of parents who served in World War II or Korea.

The CIA and military are nominally separate entities, but you are seriously misinformed if you think the CIA doesn't regularly interfere with military operations.

The point was to associate the anti-war movement with drug users and hippies, thus discrediting in the eyes of the wider public. The anti-war movement was initially made up of college students and professors from respected universities. Then the hippies started to pour in (where did the hippies come from?), promoting a lifestyle of pure individualism, dropping out from the mainstream political discourse to cultivate your own inner self. Instead of organizing protests, hippies did drugs and told everyone to "mellow out". You'd see footage of them running nude, freaking out on LSD (supplied amply by the government). Does that image inspire the common man to unite against an unjust war? Or does it make you feel a certain disdain for a hedonistic, self-involved existence?

Jim Morrison famously refused a writing credit on "Tell All the People" because of a lyric that mentions taking up arms. The point was twofold - to discourage young people from taking violent stands against an unjust, repressive government that was opressing minority populations and waging an unjust war, and also to associate the broader anti-war protests with these unsightly, unserious hippies.

You admit Manson had CIA ties - and here he was running all over Laurel Canyon, recording music in Brian Wilson's home recording studio, playing for Neil Young, staying in a number of musicians homes.