But when Superman freed the other humans she was not affected.
She wasn't with them, was she? That's my recollection -- I think I noticed that she wasn't there for the big fight and realized the writers had left her out so that she'd still be possessed after the others were freed.
Meanwhile, I'm wondering how much time passed between episodes. Last week, Sam said that going "solar flare" would leave Superman powerless for days (consistent with what we've seen in Supergirl), yet the events back in Smallville seemed like they were happening no more than a day later, and Superman had his powers back, at least partially, by the end.
Well, maybe being in the Fortress recharged him faster. Maybe that's why he was headed there in the first place.