This code is not meant to fix all the internal links on your site. Those should be linking to the correct destination. This is just to make it so that users and search engines only see a single URL per page.
Also make sure you didn’t change the order of the rules. The way I posted it only does a single redirect. If you were to change the order of the rules then if someone went to hxxp://www.website.com/index.html then it would perform 2 redirects instead of one. First it would redirect to hxxp://www.website.com then again to hxxp://website.com
By the way, I use this code on hundreds of domains and never had an indexing problem in google sitemaps because of it.