Also a word of warning: don't nuke cybie when invincible on an angel of pacifism game if you don't have another nuke for JC! You can't kill him and getting killed by JC doesn't count as a win.
It's very good advice, but... whoops my message got spoily, so stop reading until the spoiler tag works again.
I almost 'killed' JC in 0.9.8.10 during an AoPc run using splash damage, he as 'almost dead' when I died. Although I heard a rumor (could be made up) that in 0.9.9 JC doesn't take his own splash damage and only summons after he is hurt, if this is true then I don't see being able to do anything to him in AoPc. If it's not true, then it's possible, but it's of epic difficulty and luck.