I remember someone saying that the Seraphim is actually big enough to be targeted directly by the anti-capital beams, but it could be wrong as I don't know how the game would determine that.
Just for the facts: The size of a ship is completely unimportant, the tags decide how the AI handles the ship. An Icanus with fighter-tag wouldn't be attack by huge beams (although I don't know if an Icanus with fighter tag would work ^^). Karajorma already gave a good solution (didn't even now such an SEXP, script, whatever) existed.
Nevertheless, if you don't want the ships to target any bombs with the big guns ("huge") you should change it in ai_profiles.tbl (as already mentioned). Search for something like "Huge turrets target bombs" and set it to "NO".
I prefer this way because I don't see any sense in huge turrets attacking bombs, sometimes this completely changes mission balancing (remember the high damage and fire wait of those weapons).