Removing wishlist items

It should do this by default.  When you complete the trade, you should get an alert box telling you that it will add the cards to your inventory and remove them from your wishlist.  If you hit Cancel on the popup then it won't remove them.

My only other guess about why it might not have worked for you is if the cards didn't match exactly what was in your wishlist.  For instance, if you wanted a Borborygmos Enraged, and the other person had it listed as being in English while you did not, making the cards not match exactly.  I guess I haven't paid attention recently if that works or not, but I do know that it should remove things from your wishlist.