I disagree. While you may certainly argue that e.g., and aforementioned person is still reaver, Ironborn (culture) and Drowned God (religion) are – as far as I am aware – both requirements for raiding.Victarion Greyjoy pays his offerings to both R'hllor and Drowned God
Therefore, it's less about „what do you believe in” - as this seems to be small issue as long as you're not willing to burn world for your beliefs – but more about some semblance of Old Way. With mindset for raiding (Drowned God Ironborn) comes some pity for „green men”, and then green men rather doesn't like
For most part it IMHO works good. Iron Isles rarely rebel – as you said – but on the other hand, I learned to expect them to sit aside of all major wars, as they should. Ocassionally raiding would be also apprioprate, but that is more of AI deficency than anything moddable. And for the opposite far, I fould this penalty working quite good when I am LP of Iron Isles, as Kings on the Iron Throne rarely come for me, but at the same time they are quite content to e.g. never intervene on my behalf when some LP alliance comes beating at my mainland possession.
As for Stannis: yeah, he didn't rebel from religious reasons. But, on the other hand, most of his retainers were very vary of „woman in red” and burnings - and Tywin once made good use of his ways to spark rumours of intended Grand Sept of Baelor's destruction. To sum it up: I think this penalty is here to make for the distrust of your vassals, not some r'hlloran ambition to rebel. And for this, I think it works quite good.
PS. And about Iron Islanders' rebellions: I think the main fault lies with manpower. Computer just can't use Iron Isles well enough to estimate probability of success - raiding or rebellion - or just fight the war best way.
Well my "problem" with it is simply that it seems too high, not that it exists which is fine. But that is mainly a problem with the AI as you said. Although truth be told, the iron islands are OP if the AI was capable of using them correctly. In the War of Conquest scenario, i played the iron isles for fun and actually managed to beat Aegon's army repeatedly and killed 2 of his dragons, well his and one of his sisters because they have a clear manpower advantage at the start because they hold what amounts to 2 lord paramouncies right away and as such are quite capable of holding their own against any invader prior to the iron throne which shifts the balance.
Especially as a player this makes them incredibly overpowered, but the player is always at the advantage so that doesnt mean much.
But what could be done is to boost their aggressiveness to make them more "suicidal". Though i suppose you'd also have to give them appropriate boosts to stay true to the books when
20-30 ironborn manage to take winterfell
Though another thing i noticed, going through the event files, there is a so far empty plot to steal a valyrian sword, will this ever be included? I'd rather like the ability to steal one of the neat swords, although i can certainly see some problems with it if the AI keeps doing that plot repeatedly, though it would be "historical" as well since the Drumm's stole Red Rain.