Google’s John Mueller strongly recommended that those who are hit with a manual penalty should not wait for the penalty to expire. Instead, they should work to resolve why they’ve been penalized in the first place and then submit a reconsideration request.

This advice comes from the Google Webmaster Help thread that had the same topic of directories charging link removal fees.

As many of you know, manual penalties expire over a certain period of time. So do nothing and wait might seem like an option but is it?

(1) It might take six or more months for the penalty to expire. So waiting six months is often not an option for most online businesses.

(2) After the penalty expires, it doesn’t mean you won’t be penalized again. This site sells links and that is a manual penalty. The penalty expires every now and then and shortly after the site is penalized again. Don’t do what I do.

Here is what John from Google had to say:

Forum discussion at Google Webmaster Help.