I give a thumbs down to the keeping track of the points thing but thumbs up to being able to have the opportunity to tell someone they put a smile on my face, made my day or stated something very well.
Sure, you can do it in the thread or you can send a PM if you wanted to keep it private. But the rep feature is simple to use, accumulates in one place and limits your comment. Short and sweet.
The smite thing, I'm not a big fan of. You don't like what someone said and you smite them, making sure you give some BS story to support your vengeance.
When the rep points were awarded after the last time they were reloaded, people were awarded points. If the points are to stay, I say let them all be earned.