Not used this plugin yet, was thinking about using it on a domain mapped setup if I ever get it working :-) and downloaded it today (still got the issue code).
Anyway, looks like it's easy to disable, this is what I'll do before using it:
Change line 689 to
Will prob delete the yd_wpmuso_linkware function as it won't be called. That is a bizzare way to disable a link, comment it out. That is so 10+ year old SEO technique to believe a HTML commented out link would still pass SEO value! They should have gone for noscript tags if they wanted it hidden, but count SEO wise. SEO amateurs :-)
That should stop the footer link and for those with the issue of having to edit each site, no longer an issue.
You could also remove the link from the admin as well, line 662
#add_filter( 'plugin_row_meta', 'yd_wpmuso_links' , 10, 2 );
This plugin should be removed from the repository until the issue is fixed, someone who has used it should email email@example.com and report the problem. Since I've not used the plugin wouldn't be right for me to report it.