As you said, we'll see how it goes.
I like the historicity of putting resistance to boarding directly into the boarding line itself. European ships specially designed for boarding had "archer towers" on them, which made their upper decks more defendable. The added weight of building a tower on your top deck made these ships fairly slow, though.
As
@Stalker0 has said, adding plague immunity adds another level of complexity to a somewhat opaque system. You will have to be careful you don't waste attacks against a unit that can ignore your promotions. This is hard, because scanning enemy promotions with the base UI is pretty difficult, and requires you to have memorized the icons (you don't have access to the text of enemy promotions).
If promotion icons are made very distinct (unique colours, maybe purple or something?) that would help mitigate the problem. Ultimately, it will slow down combat, as players peruse promotions so they don't make a costly mistake. The other issue is that such a change will not be noob-friendly. Civ has never required such detailed counterplay