Hey, I just found your plugin and wish that I had found it sooner so as to prevent me from hacking into my core files to achieve the same desired effect!
I even went so far as to write a tutorial on how people can hack their way through the core to get this outcome! (http://eight7teen.com/articles/add-nofollow-option-to-blogroll-editor/) Man if only I had found this sooner!
Anyway, my suggestion is to remove the redundant menu item. What I mean by that is you have two menu items showing up in the dashboard... One under the "Tools" menu... and the other under the "Links" menu...
I would suggest only leaving the one under the "Links" menu as it's more relevant. To remove the other, simply delete this line of code (line 30)
add_management_page('Nofollow Links', 'Nofollow Links', 10, 'link-nofollow', 'nofollow_links_manage');