Double embarked defense is a Boolean code. I think the easiest, most immediate fix is to give naval melee/ranged/sub units a +100% bonus vs embarked units. I also agree that giving subs additional bonuses vs embarked units in their promotion tree is a great idea.
As proposed here, if there is no hard bonus for naval units vs embarked units, I simply won’t build naval units. Naval won’t be able to lay enough damage on embarked units; I will simply create larger land armies, absorb whatever damage an opposing navy tries to deal as I invade their continent, and Carry out a land war. Unless sea domain units can make utter mincemeat off land domain units, I see no reason to dilute my war production with them.