Would it make made more political sense to spare Elia and Rhaenys at least? If only to pacify Dorne and potentially adding another patina of legitimacy to the new Baratheon dynasty by jure uxoris. Tywin needed to prove his loyalty, yes, but considering without dragons, a female clamaint to the Iron Throne is hollow, would the girls provide better leverage alive?

Sparing Rhaenys would make sense – marry her to Renly down the line, strengthen your claim to the Iron Throne. 

Sparing Ellia is a good idea. The Martells are really really not going to be happy that Aegon is dead, or Lewyn Martell for that matter, but with Elia as a prisoner, they’re not going to make noise over it while she’s alive. Then again, if you believe Tywin, he didn’t want her dead.