Why not just run 2 MSN Messengers?
I know its really annoying when windows messanger starts same time... There is a way to remove windows messenger tho.
Start->
Run->
RunDll32 advpack.dll,LaunchINFSection %windir%\INF\msmsgs.inf,BLC.Remove
If you have SP1 (Service pack1) You'll get an OCX not registered error. Just click ok and it'll be uninstalled anyway
Hope that helped.