I like this rule, it's plain, it's simple:
FINISH IN TIME!
Tourney deadlines are transparent, you see the clock in RGs and CC tournaments, you (should) know when midnight is in WGT town for the weeklies and such - the rest is up to people responsible for their actions. Why mess around with this? This feature works, why risk any betterworsening?
I remember entering a tourney late - I used the ball speed boost and I knew I'd be told on the last shot whether I made it or not. I think, not - my bad.
And, what's the crying about the ball usage (don't forget the boost)? They were used, fun and excitement were received from the game, should it not be payed with a few Cents for ball life?