How could Aegon V accept Lord Lyonel Baratheon back under the King’s peace alive and in power? As Robb Stark said: “My lord father taught me it is death to bare steel against your liege lord.” At the most merciful I could see Lyonel take the black.

Because in the middle of an ongoing civil war with the Blackfyres, Aegon didn’t want to fight one with the Baratheons. Lyonel would definitely fight to the last, and in the Stormlands, that means a half-hundred grinding sieges. 

Luckily, Lyonel agreed to a trial by combat.

Also, Aegon V knew that he was sort of in the wrong, even if Lyonel was taking honor to an extreme.