Are you sure that is the case? I believe there is also absorption by the intestines. For example, in a previous thread one of the posters on this forum said that eating lobster helped her a lot and later discovered through experiments that the key was the threonine level in the lobster. My understanding is that the food provides the nutrients to the lining via digestion and having foods high in amino acids (that are healthy for the lining) are delivered directly to the lining through the food.
Even if this were not to be the case, and if most of the amino acid does go straight into the blood, it would still have to go through the liver. Hence, I think the benefit of a suppository delivery would deliver more of the amino acid.
Unfortunately those amino acids don't go straight to the area.
They will get absorbed into the blood stream, and are then used by the body in the normal way. It's probably better to simply eat more complete protein.