"But Lee isn’t taking the thing down"
Good for you.
Hosting a shell script with informative keywords seems like completely reasonable fair use, so if this goes to court, I doubt they will have a case.
The site fixubuntu.com doesn't appear to have any logos on it now, maybe it did before? So at the very least, it looks like he pulled that, if they were there in the first place. This article seems to imply the logo was there.