You could use the right-click the window's switchbar button and select "Desktop". Right-click again and select "Position > Save". now its on the desktop, but swicth it off the desktop or what ever, but dont save it.

Now you could use this sequence but well need to check if someone is already in the channel so it only does it if there the first join, the check needs to be either 1 or 2, one being just you in the chanel, but it might be 2 if its already added this new person, so try 1 put if it doesnt work try 2.

The idea is when someone joins and your the only current ONE in channel ( or now theres only TWO of you ), you actualy leave the channel close the window, and rejoin the channel, this well cause the desktop setting to be applied, but well clear the channel, you can add code to cacth the channel contents and restore it if thats important i guess.

on *:join:#channelname: {
if ($nick(#channelname,0) == 1) {
part #channelname
window -c #channelname
timer 1 1 join #channelname