Does defying or playing a rebuttal on a spell played from flow still banish the spell?

Yes — a countered Flow spell is still banished, but only when it's actually countered.

Flow's banishment is a delayed replacement effect (Rule 829.1.b.1): any time the spell leaves the chain as a finalized chain item — except by resolving on its own — it's banished instead of trashed. A counter (Defy, or Rebuttal's "otherwise, counter it" branch) sends it to banishment, not to the trash. The counter also means "when you play" triggers won't fire and costs aren't refunded.

One exception: if Rebuttal's controller pays [A] and takes control instead of countering, the spell isn't countered — it resolves and then goes to its owner's trash normally, since leaving the chain was instructed by its own execution. (Rule 829.1.b.1, FAQ #11690)