This. I is hard to believe that Gregor helped Elia and Aegon to escape. If he didn't, recognition of dead bodies was left to a chance. On the other hand, the possibility that body doubles were just left to die, depicts Elia and her supporters in most awful way.
Maybe we can look at the situation considering that all players acted on their own motives each and didn't just follow scenario of one person.
Elia's and Aegon's doubles were not supposed to die, they were left only with intention to delay pursuers. Lannister soldiers probably didn't know how exactly Elia looked. Elia's supporters expected soldiers to bring fake Elia and Aegon to Tywin or his generals, thus giving Elia time to escape.
But they underestimated Tywin, who was cat of different coat. Tywin just simply ordered to kill Rhaegar's children. When he was talking to Tyrion he admitted that with ease, but he didn't admit he ordered to kill Elia too.
Gregor went on his task. Elia's double in face of death revealed the truth to him. What Gregor did? Gregor was a simple person. He just crushed her head that nobody would know about the swap, Tywin in the first place. Thus he completed Tywin's task. Tywin and Robert Baratheon were content.
Maybe, only maybe, it was Gregor's some strange and tiny tiny expression of loyalty to Rhaegar, who knighted him. By killing doubles he gave Elia chance to escape. Of course, he didn't cared about some baseborn woman and child. Remember how his more scrupulous brother killed Mycah.
I see this as possibility to explain why Elia and Aegon were unrecognizable, but it doesn't explain why Elia left Rhaenys. And why she never contacted Doran and especially Oberyn, who was told to be very close to her.