We had a similar issue with DS -- he hated applesauce AND he hated pregistimil (formula). Life became much easier with baby food bananas and regular formula.
I know he's only two, but is there any way they could try to give him the whole capsules to swallow. DS started taking pills when he was 3 or 4. Or maybe give him some control and let him choose how he gets his enzymes, let him sprinkle the enzymes on ketchup, jelly, maple syryp himself and put the spoon in his mouth himself.