We talked about the last point once. In fact it was me who brought up that Ferdinand and Isabella's marriage was the most repudiable marriage ever signed since it was illegal. They were cousins, used a fake papal bull and married in a kingdom whose king (and Isabella's liege lord and head of her house) had forbidden that marriage from taking place.
But if we look at the situation at the time we can see, instead, that keeping the marriage would actually benefit both Aragon and Portugal's interests in the long run, and they would know it. I explain:
The war wouldn't be over in a matter of weeks, so the 1475 births of Ferdinand and Isabella's first daughter and of the future John II of Portugal's son, as well as John's sole sister entering a convent and refusing any marriage prospect would not be butterflied.
Aragon would need to break the French-Portuguese-Castilian alliance ASAP. Best way to do it would be to sign peace with Portugal and enter into marriage negotiations.
Aragon might do a 180º, repudiate Isabella and marry Ferdinand to a French princess. But that's unlikely. Too much recent beefs, too many ongoing conflicts. Aragon cutting a deal with Portugal is far more likely. After all, once the succession matter in Castile is settled with a Portuguese victory Aragon and Portugal had no more clashing spheres.
But Portugal has not a wife to give Ferdinand. However, both parts can agree on the marriage of John's infant son and F+I's infant daughter (thus keeping F+I intact) in the peace treaty as IOTL. This way:
- If Joanna and Afonso V have children, they inherit Castile only.
- If they don't, succession in Castile goes back to Isabella and her daughter. Married to John's son, that makes him future king of Portugal and Castile (and she Queen of both, plus Aragon).
- If F+I have no male children Aragon, Castile and Portugal end all ruled by John's putative grandson of the Aviz dynasty.
- And if all marriages do produce children, the three remain independent but tied by dynastic marriages (granted they all had that before and it was how the war started, but whatever).
Portugal has no use for France's limited and self interested help once the war is over. A marriage with Aragon is too good of a deal to pass it, and if they ever come to clash with France an alliance with Castile and Aragon would stop it on the Pyrenees so it is not an issue. Not that Portugal and France's spheres clash either.
Massive changes would happen anyway. For starters, with Castile ruled by a Portuguese king, no one would bouch for the Castilian-Portuguese dispute over the Canary Islands to be resolved on Castile's favor.
While Afonso could live a few extra years without the Castilian defeat taking a toll on him, he might be too old to have children by the time Joanna is capable, and he would be a vulnerable foreigner that would need the support of big Castilian houses to rule anyway. The real master of Castile would be the ambitious Archbishop of Toledo, Alfonso Carrillo (d.1482), and after his death his grand-nephew the Marquis of Villena (d.1529) whose family's massive lands and wealth would have not been seriously curtailed by Ferdinand and Isabella ITTL (and if anything, would have increased, since Villena would have not lost his bid to succeed his father, an enemy of Isabella, as Master of Santiago and would have administered all the order's lands as well). Joanna seems to have been as docile and easily manipulated as her (questioned) father, not a fighting spirit like Isabella.
Bad times for Castile ahead. The path to absolutism blocked, nobles in real control of the kingdom, no military orders absorved into the Crown (who would destine their great resources to intrigue within Castile since the Moor has not been a danger for centuries), colonial interests cancelled and given away to Portugal.
Meanwhile,
1) Aragon might lack the strenght/security to go in Italy as far as it did.
2) Granada could have a shot at survival. While the king would still idiotically go to war with Castile in 1481, someone who had not Isabella's enthusiasm would give up by 1485 with some territorial gains and one of the three contenders for the Granadan throne as a puppet in the rest, rather than pushing for total conquest.
3) Navarre would also get a shot by playing Aragon's interests versus Castile's, which IOTL obviously couldn't after Castile and Aragon united and eventually lead to its puppetization and annexation.
4) The Inquisition would still come (Carrillo wanted it) but the Jews might not have to convert or go (the lovechild of Isabella's Christian naivety and Ferdinand's antisemitism). No great reforms of the Castilian church by Cisneros however, which are credited with preventing the Reform from taking root in Spain rather than the Inquisition - which would be very weak compared to OTL, a historical oddity more than anything else.