Recently Andrew Connell has posted an article about the proper way of overriding the Render methods while inheriting from the WebPart class. Andrew has pointed out that it is very important in order to preserve the working of the Web Part Page Services Component (WPSC).
No matter the circumstances it is always the Best Practice not to break any of the standard functionality. You might not use it just right now, but are you sure you're not going to use it in the future? One of the scenarios when breaking the WPSC is accessibility: in order to make the content of the Web Parts accessible you need to remove the tables rendered by the Web Part Zone. So far there is no other way to do - at least not that I know of.
It doesn't really matter whether the choice for breaking the WPSC is right or wrong. What does matter is that you make an educated choice and are aware what the consequences are. Unfortunately there aren't many sources on the Internet on what WPSC actually is and what it makes possible. Also the available literature doesn't present the contents and possible usage of WPSC.
Eugene Katz has just posted an article on a scenario he used the Web Part Page Services Component in his project. Reading it might give you a better understanding of what WPSC actually is and what you can or cannot do with it. This should eventually lead to making the choice whether you should preserve it or not easier.