You should call Delta and ask if they have an interline agreement with Air Malta. They probably do...

If so, and you can check your bags all the way through then you're still going to have to clear immigration in Milan and then go to the A (Schengen) area.

You can check in online with Air Malta so theoretically you could do this IF your bags are transferred AND you have a boarding pass. Otherwise you will have to go out and recheck in. You really only need to be at check in for Malta one hour before so I think that it's adequate time regardless.