The best unit that I found so far against elephants in MTW2 is javelin armed cavalry(Jinettes, Polish Nobles etc), javelin men work, but take high casualties and usually rout a couple of times. As you are playing Milan, I would suggest trying artillery, or try recruiting some mercenary elephants of your own.(available around the Baghdad area I think).
Muskets would probably work against them, but I have never had any when I've come up against Timurids, so you'll have to try them yourself.