Thawne did also [as I remember] mention that him changing things had consequences he is having to live with when he was advising Barry to think twice about going back to change the past. Though Thawne has done bad things, he knows more about time jumping than any of them. I was also shocked though he didn't at least try to talk to her more or do something to ease her pain. Just let her lay there and die like the 1st time around.
Maybe you confused it with Arrow?
Arrow is about to air its 4th season. The Flash is a new show!