I've been successfully running this patch on a production server for two weeks, and we haven't crashed again, so at the very least it is a workable solution.
My WP is set up as a CMS also, and the permalink issue only comes up with posts, not pages, so you should be fine. My pages at the root are /about, /share, etc. Only the blog, which is set up at /listen, is affected by the permalink issue. So individual posts are /listen/2007/post-1, /listen/2007/post-2, etc.
Since our site was new, moving to a new permalink structure wasn't such a big deal, for those with more established blogs I imagine it might be a problem. The are supposed to be permalinks, after all.