Yes, he did push the Commerce Clause beyond anything that had been done before.
But he would not have had to do so were the situation not so dire, and if there already was a network of State regulation to work with. Lochner made sure that not only the Feds couldn't "interfere", commerce clause or no, with labor relations, but States couldn't either.
There was no Federal "usurpation" when FDR did what he did. There was not a skein of State law swept aside. Thanks to the Supreme Court, the States hadn't been allowed to develop any sort of comprehensive law in the whole field. FDR was facing a national disaster and mortal foreign enemy, and rising internal tensions of really desperate people, and he had to start from scratch.
What was he supposed to do? Wait for the States to cobble something together? But the States were not able to rise to challenge Lochner. It was FDR and his New Deal that kept getting shot down by the Supreme Court. There was no time on the clock. Social tensions were rising to the bursting point in America, and the Nazis were on the march. FDR needed a functioning American economy, he needed to defuse boiling social tensions, and he needed to do it FAST because of impending war.
The Supreme Court created the mess with Lochner. FDR had to lead the country out of a mess in a hurry, and the Nazis and Japanese were not going to give us the luxury of time.
The depression was global. Nothing FDR did helped one bit, and Wickard v Filburn didn't have anything to with labor unions.