Yes, the Iberian situation has taken a surprising new twist since Aug 15th...
Whilst I agree with the logic of giving Castile and Leon claims on each other, and Navarre and Aragon likewise, it does mean that half of the Christian kingdoms are condemned to death within the first 20 years. In fact, I've yet to see a game where all four survive longer than 10 years - not from muslim invasion, but from conquering each other.
The muslim infighting seems to have got a little more rampant in the latest beta as well, or maybe that's just the games that I've seen, but generally what seems to happen is that Iberia is now structured to create three or four interim powers (generally Leon-Castile, Navarre-Aragon, Cordoba-Granada, Badajoz-Sevilla) which then go on to narrow themselves down to, normally, two Iberian superpowers.
Short of dramatic foreign intervention, normally one religious group overwhelms the other due to alliances being called in - and all this normally happens in a very short space of time.
I'm trying to think of anything which could be done as a specific set of Iberia events, but nothing leaps to mind. The wars between ALL the nations there are generally so quick and so decisive that there's not much that you can do. Punishing the victor afterwards by having evil events trigger for non-matching ruler-province religion or culture would help stop superpowers forming, but since the victor would hold both kingdom / realm titles then its unlikely that vassal breakaways would lead to, say, Leon fighting off their Castilian conquerors and putting a new king on the throne. In fact, they'd fight off their Castilian conquerers and then lovingly repledge loyalty to them, which rather defeats the point.
Plus, the muslims wouldn't be as badly affected since they all share the same culture. Grr.