Eobard had been expecting Barry to fight back. It wouldn't have been any fun if he hadn't. What he hadn't been expecting was the power behind Barry's punch, the crackle of the lightening driving his momentum. There was something here that he was missing, but there wasn't really time to think about it as he crashed into the ground. Recovering swiftly despite what felt like a fracture in his arm, Eobard hugged the limb to his body as he rushed at Barry. It would knit quickly enough, but until then, he was going to be slightly hobbled in this tussle.
"I'm the sanest person alive, Barry," Thawne said, the lightening crackling over his body as he wound up his uninjured arm. "You have no idea what you're facing. This will be a mercy. So hold still."
It was the opposite of what he was used to telling Barry, but right now, he didn't need him to run. He didn't need him for anything anymore. If he'd failed in his plan, there was only one thing left for him. Killing this Flash, this Barry, wouldn't be nearly as fulfilling as killing the one he'd truly wanted to. But he'd already made that compromise when he'd gone back in time initially. This was just a further extension of that.