Eobard Thawne aka Reverse Flash wasn't there to kill Barry's mom. He was there to kill Barry Allen. But Flash followed him through the speed force and took his younger self to safety. Boiling with anger thought of another way which could change the event in such manner that, Barry Allen never gets his power. Reverse Flash believed that the shock of his mom dying would prevent Barry Allen from becoming the flash, So he killed her. But when he tried to run back to his timeline, Thawne realized he lost his connection to the speed force. So, In order to return to his timeline, he had to be the one to make Barry Allen The Flash.