“In terms of weregild, would a Rhaenys-Robb or Rhaenys- Renly match...”
Could it not be argued that Jon/Daenerys would be a fulfillment of that pact as well? Now, both are Targaryens, but Jon is a Stark as well. He could be fostered for a time with his uncle, creating a connection between the two houses. And Jon would probably take more after his mother and uncle than his father anyway, not just in looks but in manners as well.
Jon is a bastard whereas Daenery is a princess, who is going to argue for a match between a bastard and a princess, even if they share blood? Certainly not Princess Elia whose son can be endangered by his half-brother (the history of noble bastards troubling half-Martell Targaryen monarchs is infamous and bloody) She is not going to give Jon a princess bride to bolster his acceptability.
Too, while I avoided mapping how this au would work (because it’s very complicated and would require too many shifting pieces) and only answered the question as was presented, I’d think that any negotiations between the royals and the rebels would have to happen before Ned even found out about Jon. And it wouldn’t be that easy for Ned to foster Jon in Winterfell (unless he still conceals his paternity) because again, the Blackfyres would leave Elia wary of leaving Jon with his maternal family who just waged war against the Targaryens.