The only way to be really sure whether autism is caused by MMR would be to do a massive trial, with thousands and thousands of children.
Put the kids into one of 2 random groups. Give one group MMR, give the other group single measles / mumps / rubella vaccines, and make sure neither the children's parents or the nurse administering the vaccines knows which group is getting MMR and which is getting single vaccine. Administor placebo shots as necessary so each group gets the same overall number of jabs.
Then, a few years down the line, see whether there's any difference in autism diagnosis between the two groups.
It's highly unlikely anyone's going to do a trial like that though.