"Because the author has removed major characters which they can't legally use in their derivative work, then that work should be excluded from the wiki."
I wouldn't say they should be excluded from the wiki, even if they are not considered valid sources.
"It's not at all like K9 where there are just no clear references to the DWU, and the established DWU is often contradicted. Nor is it like Vienna, where Big Finish are clearly in the position to make it a DWU series, but have explicitly decided to go in a different direction."
OK, but why is then K9 covered, if it's contradictory to the established DWU and is not an official BBC-licensed spin-off? Also, I don't think Iris Wildthyme audios are really a Doctor Who spin-off, given that her character predates her inclusion in Doctor Who media, and I don't think her own solo stories actually reference the DWU. I haven't listened to Vienna yet, on the other hand, but it looks like her first solo adventure has quite a few references to Big Finish Doctor Who continuity, even if they don't mention the Doctor himself.