If you render your XHTML property using @Html.PropertyFor(....) any links will be parsed by Episerver. If you are working with the property html directly, you need to this your self by creating a helper method that parses the html and replaces the guid based links with friendly urls. 

The internal url is a good idea to keep since otherwise you will create a lot of 404s if you change urlsegment or move a page/media in the structure. So you probably want to keep it and resolve the friendly url later in the chain instead...

With this specific xhtml editor i need to save it to a seperate database for use in a tool i'm working with so @Html.PropertyFor won't work in this case sadly and this tool won't be able to translate the internal url to the friendly ur.

I would then convert it before saving it. Something like:

        public static XhtmlString ToExternalLinks(this XhtmlString xhtmlString)
        {
            var result = new StringBuilder();
            foreach (var fragment in xhtmlString.Fragments)
            {
                var urlFragment = fragment as UrlFragment;
                result.Append(urlFragment != null ? UrlResolver.Current.GetUrl(new UrlBuilder(urlFragment.InternalFormat), ContextMode.Default) : fragment.InternalFormat);
            }
 
            return new XhtmlString(result.ToString());
        }

Then I guess you need parse the html before saving it in the database (you can use Regex to find links in the html).

Thanks Daniel Ovaska! worked great!

Sweet!