While still shocking, I expected the Sybil system to be something like that, after all this is a 'dark' anime.
Makishima was given the choice to become 'god', but he chose to stay as a player in the game of life. Guess being purely a passive observer was too boring for him, Touma Kouzaburou misjudged Makishima's personality and ability big time.
While I'd like to believe Touma 'died', he probably has backups in the Sybil system, so he'll appear again.
Someone said in the previous episode thread that there's an army of Chief Androids, guess he was right.
Since Makishima rejected their offer, Sybil system will probably update itself and make him a killing target, regardless his Crime Coefficient.
Personally, I suspect Kogami will team up with Makishima later and take down the Sybil system. At the very least, Makishima thinks extremely highly of Kogami, since he even went out his way to contact him.