Neither one of these places sounds very desirable. Is there no other barn you can get lessons at? My instructor has been great about flexibility in scheduling, and (she's also the barn owner) the horses are all in very good condition. Some of them need to gain a little weight, but that is an issue she is open about and is actively working on with the vet. I have never seen a horse whipped at this barn. Crops and dressage whips while in saddle, yes - but even then, only as a reminder, not a punishment. Even when my mount is being truculent and uncooperative, it's always clear that this is the rider's horse management issue, not a fundamental problem with the horse.
If you've got to pick one, I'd say go for the one where the instructor was a jerk about the time (and see about getting a different time slot) and not the one where the horses are mistreated.