Here (http://www.delicious.com/csad/bundle:startrek%3A2009%20episode-tags) are a few stories I found with TOS episodes/scenes rewritten.
As for femslash, I would suggest going through AO3's tags, for example Gaila/Uhura (http://archiveofourown.org/works?selected_tags[tags][]=9630&selected_tags[tags][]=9833&boolean_type=and&tag_id=Star+Trek+%282009%29&commit=Filter+Works), since I have this strong suspicion none of the stories there will ever be badfic (or at least I have yet to see one there, so I could be wrong).
no subject
As for femslash, I would suggest going through AO3's tags, for example Gaila/Uhura (http://archiveofourown.org/works?selected_tags[tags][]=9630&selected_tags[tags][]=9833&boolean_type=and&tag_id=Star+Trek+%282009%29&commit=Filter+Works), since I have this strong suspicion none of the stories there will ever be badfic (or at least I have yet to see one there, so I could be wrong).