Charles made the Burgundian match who was arranged for him and who he wanted for the interest of his native land. And Joanna REFUTED to give ANY help to the comuneros OTL and would surely do the same ATL
He did. I would say personal feeling weighed less into it, and more of political considerations. It is definitely not a bad marriage, just a different one.
You are correct in that Joanna refused to aid the rebels, but I don't like relying plainly on our time period for reference for an alternative time period. It's helpful, yes, but we aren't bound to it. That's the whole reasoning for alternate history, to explore other possibilities, and for entertainment. People make choices for a variety reasons. Hindsight allows us to see things that aren't evident to these people at the time they make those choices.
On top of that, there's no denying that Joanna, whatever political / sexist propaganda might've been hurled at her in this period, there was no doubt that she was a woman who was severely mentally ill. Her grandmother had been mentally ill, and mental health issues were common amongst both of the Iberian royal houses.
The point I'm trying to make, is that someone in a situation such as Joanna's is perfectly capable of having lucid moments and making the "correct" decision, just as she was perfectly capable of making a disastrous one. Obviously, what is correct and disastrous are completely oblique terms; before the comuneros stormed Torsedillas and basically demanded Joanna's support, a royal delegation had arrived previously asking her to denounce them, which she demurred from doing, wanting specific terms.
Adrian of Utrecht, along with her confessor, and Ocha de Landa managed to convince her that supporting the comuneros would be detrimental to Charles' reign, but given the lengths they had to go to secure her noninterference, we cannot be surprised that Charles tightened the rules on her confinement in the aftermath of the revolt. She was clearly not a person on whom Charles wanted to rely on, because she could've just as easily given her support to the rebels. Unpredictable people can make unpredictable choices.
No way who Charles would let Ferdinand to remain in Spain. He would be sent away shortly after Charles‘ arrival there as OTL. And remember who in OTL Charles married Isabella of Portugal only in 1526 meaning who he had nobody to cover her role before that date. Plus Ferdinand is destined to marry Anne of Bohemia and Hungary as soon Ferdinand of Aragon died (another reason for sending the boy to Maximilian as soon was possible)
Who's to say what might happen? Margaret initially didn't even want Charles to go to Spain following the death of Ferdinand, and many in the Castilian government feared the influence of his Burgundian entourage, for they feared he might favor the French and make decisions that went against Spanish interests. He was certainly in no rush to get to Spain, he only reached there towards the end of 1517.
Ferdinand was sent away because of the marriage plans for him, but there's no concrete evidence that he was sent away because he was a threat. Even the most well laid plans can blow up in our faces, after all.
In what way is Ferdinand destined to marry Anne of Bohemia and Hungary? Destined seems like a very strong word. Any number of things might've came between the marriage. She could've died young. He could've died young. Maybe her parents decide to dedicate her to a religious life (not uncommon amongst the Jagiellons, even those 'early' in the birth order). They could've easily ended up with a childless marriage. Mary and Louis II might've been the ones to have several children. What played out in our world allows us to see that it was an advantageous marriage for the Habsburgs. But at the time the betrothal was made, few had any idea that Louis II of Hungary would go and get himself killed at Mohacs and pass his kingdoms to his brother-in-law. At the time? A good marriage, but not something I'd say was destined; destiny and history are two different things.
They weren't married until 1521 (I've seen 1515 claimed as well, but given her young age, Ferdinand's young age + being in Spain, I'm assuming it was a proxy marriage). We all know from Anne of Brittany's experience with Emperor Maximilian that proxy marriages don't hold weight. Betrothals are broken just as easily as they are made, and there are plenty of royal princes and princesses that can attest to that.