
The wiki seems to have been defunct and many articles are written poorly, regardless of the canon. And yes, the canon tags are used also poorly but it's not something that can't be fixed. The best articles (and "Bronso" that was mentioned above) use the tags in a clean way; as DuneFish said it's as it should be so here is an example. Perhaps you don't like the reference that Paul joined a circus, but this sentence is where it should be, and it's not mentioned in the Dune novel timeframe.
I think that when it comes to FH's works the Dune Wiki sucks but that's simply because many articles were copyedited from Wikipedia with no serious editing effort. Wikipedia articles were written for "Dune characters" and not for personalities with real biographies. It's not something irredeemable.
Furthermore, since it is "Dead" you should not be afraid of edit wars and stuff.
So I would say "go for it"
However I expect that all canons (like "official authorised fanfic") are respected.
I have wasted some time there editing some detailed Butlerian Jihad articles as presented in LoD. I would hate seeing all those paragraphs I wrote, purged or reduced to a small references in a "Behind the scenes/No-canon" section by a fanatical purist who considers it a blasphemy to coexist or even exist.
I believe the two canons can co-exist without meddling with each other. There are a lot LoD articles that can stay there without harming anyone. There is also information on the Dune Encyclopedia which is so favorable here (eg. since you don't like the Butlerian Jihad article see here: http://dune.wikia.com/wiki/Butlerian_Jihad/DE). There are articles about Dune Encyclopedia and even the video games.