This thread has become a bit embarrassing hasn't it?
Cerebo is a device that can reach into people's minds and needs a telepath to power it. Apocalypse effectively hacked into it while Charles was using it. I guess the black eyes represented those connected to Cerebro while it was corrupted. Charles himself wasn't controlled by Apocalypse at any point, hence why he asked Havok to destroy the machine so Apocalypse couldn't use it to do further damage.
Charles also wasn't controlled by Apocalypse when he was forced to do that speech. That was good ol' fashioned intimidation. Charles complied so he could use the power boost to reach out to Jean for help. Once he was done, Charles flipped the script and gave Apocalypse the proverbial finger.
This is something I've seen a few times that really doesn't bother me. Apocalypse has a massive god complex and believes that the most powerful should survive. He despises the idea of weapons as he sees them as a tool that the weak can use to level the playing field. He could turn them around on their wielders, but it would be counter to his values.
Singer said he based the horsemen on the four pillars of a cult: Military (Archangel), Politics (Magneto), Sex (Psylocke) and Youth (Storm). Sounds better in theory tbh, I didn't get a whole lot of that out of the film (other than Psylocke being hot).