With the current settings, a comment has a day to make it out of pending. If you delete a pending comment, it's no longer pending.
Edit: Deletion is currently possible for less than that (2 hours?). Will this be different for pending comments?
On a related note, the new system may prevent people from posting in the feature suggestion thread (https://news.ycombinator.com/item?id=363). Since it's already a special thread that never closes for comments perhaps comments posted there should not be made pending.
I suppose that the 24 hours is a parameter that is easy to change and tweak. I think it's a lot of time. What about 1 or 2 hours?
Another possible idea is to have up to two pending comments, so someone can contribute in two threads, go to work/eat/sleep, and read the replies. But this version is more difficult to implement and more difficult to explain.
Also some visiable indication on near the user/logoff part of the page indicating if can post or awaiting approval of a pend - say a "+" indicating can add a post and a "-" indicating you can't as have pending post.