Yeah, I usually leave the points alone. But points are only cosmetic. I see it as "3 strikes can be enough" -- but really, 1 strike can be enough -- but before taking serious action on anybody, I make sure to review their history. This means looking at what they got warning points for. If it's minor, I ignore it. If there's other history not recorded there that I'm aware of (for instance, discussion here), I'll look that up, or make a post and defer to you guys' thoughts.
As far as I know, removing it won't clear the record of the warning, it'll just reset their point count. So nothing would change; you'd still have to go through and see what all the warnings were for!