Let’s say Gregor and Amory Lorch don’t kill Rhaella, Aegon, and Ella during the sack of KL. They instead keep Rhaegar’s children and wife hostage and present them to Robert Baratheon when Robert enters KL. What does Robert do? Can he afford to let Aegon live?

Aegon alive is the biggest danger. Rhaella can be married off to Renly to merge the two claims, but Aegon is a rallying point for Targaryen loyalists. 

Best-case scenario: Robert has Aegon held captive, so that Viserys can’t be the rightful heir, until Aegon is dead.