Premature pulling out is never recommended....
That being said, it shouldn't ruin your battery. Did you try just draining the battery or plugging it back in. I am not sure where it mentions draining the battery by running the quad with the props off as that is actually really bad for some motors. Maybe the tolerances here are different from what I am familiar with but just check the manual before you go and do that. The motors will run much faster and therefor much hotter with no prop to slow them down.