This is relatively untested, but I've found that by changing the following line of code, I was able to add relative urls as links in wymeditor.
backup then open:
wymeditor/jquery.wymeditor.min.js
find:
var sUrl=jQuery(wym._options.hrefSelector).val();
replace with:
var sUrl=jQuery(wym._options.hrefSelector);
I accept this is probably not an ideal solution, as it appears to be removing the 'validation' part of adding a link url, but it seems to work all right.
Warning:
This is only for urls in hyperlinks - not for image filepaths and such.
This may allow your users to add crap to your pages in the hrefs of links.
Always make a backup first.