They killed Elia’s husband who had just publicly humiliated and discarded her, and put her in power over the Seven Kingdoms. She’s not necessarily their friend, but I don’t see how she’s their bitterest enemy, either. Put in Jon Arryn as Hand of the King, and put a couple of other prominent rebels on the Small Council, and you’re not necessarily in a terrible position.

I’m sure Elia was angry with her husband – but she’s not going to be friends with his murderers, the men who sacked King’s Landing and murdered the King, who killed her uncle and thousands of her countrymen, and who are holding her and her children hostage. 

This just doesn’t make sense by anyone’s political interests. The rebels have absolutely no reason to keep the Targaryens on the Iron Throne when it means an enormous risk that an adult Aegon VI will have them all executed for killing his father, and Elia has no reason to work with her enemies.