Maybe something like /writeini -a<C> which will append data to an already existing item.
Example:
[#Channel]
Users1=ChanServ,OperServ
Users2=ChanServ OperServ
/writeini -a44 Channels.ini #Channel Users1 Jigsy
/writeini -a32 Channels.ini #Channel Users2 Jigsy
[#Channel]
Users1=ChanServ,OperServ,Jigsy
Users2=ChanServ OperServ Jigsy
The only current method of doing this is by re-adding the previous data along with the new data.
/writeini Channels.ini #Channel Users1 ChanServ,OperServ,Jigsy
Etc.