Well parts of Defending the Earth!, as I'm sure you know all too well, have been edited by and comments have been added by the general public. If we would make that a valid in-universe source, then I can go there and post something utterly preposterous like, "I'm the Twelfth Doctor. I have ginger." and all of a sudden, we'd have to create the Twelfth Doctor and add that he's ginger. But, no, that's ridiculous. So that's one aspect that definitely cannot be valid. Also, the UNIT site only adds to the UNIT dating controversy. I'm also sure that a lot on the sites (even the parts written by BBC) explicitly contradicts the TV stories.
But I have one last point: these aren't necessarily "in-universe" pages. They can also be considered out-of-universe fictional websites based on the in-universe websites, and hence we'd have two different websites for Who is Doctor Who? (Rose) and Who is Doctor Who? (web) or something like that. The former would only talk about what we know about the website in-narrative, as the website that Clive Finch created because he noticed this Doctor that Rose noticed, whereas the latter would talk about the out-of-universe website that the BBC website put up and treat that information in the same way that we would The Brilliant Book 2012. Just putting my two cents in, whatever they're worth (I'd imagine about two cents...).
CORRECTION: They might not be worth two cents, but they'd be Canadian and Canada Mint has recently abolished the penny. Everything's rounded to the nickel now.