It is still possible it isn't a penalty from one of the major algorithms and you may be able to solve this by creating a strong internal linking strategy. It helps to formulate one if you use something like MindNode to create an overview of the site and then you can drill in on the pages in questions.
It is possible that a noindex would cure this, but it all depends because even though you add a noindex tag to a page, Google can still read the page and apply the penalty. All it means is that the page won't be indexed.
However, if you are relaunching everything very soon, you might be as well to sit tight and not do anything too rash for a short-term solution.
-Andy
