Use some lightIRC javascript snippets for your own. Don't forgot to set true on loopClientCommands or loopServerCommands, depends what you use.

Javascript Snippets lightIRC.js

// #1 - Javascript snippet to let users join allowed channels only - See: http://redmine.lightirc.com/issues/647
function onClientCommand(command) {
    var raw = command.split(' ');
    var chanArray = ['#test', '#test1', '#test2'];

    if (raw[0] == 'JOIN' && raw[1].charAt(0) == '#') {
        if (chanArray.indexOf(raw[1]) < 0) {
            alert('Sorry, this channel isn\'t allowed');
            command = '';
        }
    }
    return command;
}