I didn't read throught the thread very closely.
Maybe you could put it back in and just keep people from joining #chat and #admin.
Aside from #admin, if Ephi's going to be blocking out official centralchat channels, he could just have it read from the MOTD (372):
[15:24:46] :scruffy.centralchat.net 372 []TruceBot :-
[15:24:46] :scruffy.centralchat.net 372 []TruceBot :- Official Channels:
[15:24:46] :scruffy.centralchat.net 372 []TruceBot :- #chat - general discussion
[15:24:46] :scruffy.centralchat.net 372 []TruceBot :- #harrypotter - harry potter chat
[15:24:46] :scruffy.centralchat.net 372 []TruceBot :- #helpdesk - technical support
[15:24:46] :scruffy.centralchat.net 372 []TruceBot :- #runescape - runescape chat
[15:24:46] :scruffy.centralchat.net 372 []TruceBot :- #uno - online uno game
[15:24:46] :scruffy.centralchat.net 372 []TruceBot :-
(Log was from about 7.5 months ago so it could be a tad different.)
EDIT:
Of course, anyone who could re-enable /join before could probably take out the filter as well.