Didn't Aerys insure that Elia and her children remained in King's Landing during the rebellion as a way to vouch safe that Dorne would stay loyal during the Rebellion?
I don't know if it's ever explicitly stated, but it sure reads like Elia was being used as a hostage to force Dorne to back Aerys. What Elia thought of that, if Rhaegar had explained everything and she for some reason was totally into his whole messianic fucking of other ladies, or if she was waiting for Doran to storm the gates and save her from this nightmare, I'm not sure we'll ever know. The fact that they always seem to emphasize Elia's sickliness makes me think Rhaegar was never really satisfied with her, which I would think wouldn't lead to a happy Elia, but again, who knows.