The "penalty", as I understand it, is neither a fine nor a record of wrongdoing, as paying at the end of the year is not illegal. The penalty is the IRS saying that it would like to have the interest back that it otherwise would have earned if you had paid earlier.

As far as I understand, it's perfectly kosher to wait until the end of the year to make payments; you just have to make sure you have the money to actually pay then.

Disclaimer: I am not an accountant nor do I have expertise on this matter.