chrisv1963 - 9:14 am on Mar 1, 2011 (gmt 0)
My site that got hit has a lot of links to other site sections
This should not be a problem. Matt Cutts always said that you should make a website with your visitors in mind. With links to other sections of the site you are making it better for visitors because you are showing them the way to more pages on your site that are relevant.
When for instance I write an article about "blue widgets", I would link to an article about "how to make widgets blue". This is perfectly normal linking.