I don't think he's proposing rewriting Tolkien to establish a canon, but rather pointing out the consequences of an attempt. There was so much work Tolkien did behind the scenes in producing his completed works, that any attempt to bring his more incomplete writings into a canonical framework would take several lifetimes. He was given only one lifetime, and we should be grateful for that.
There is so much wonder and beauty in The Silmarillion that I feel it's better just to have it, as non-canonical (in parts) that it is, than to never have had it written in the first place. Who knows what wonders might have been produced if Tolkien came to fame (and fortune) twenty years earlier than he did?
I think what Tolkien's son was trying to do was cobble together all those notes and sketches and excerpts etc together into some credible format for fans to get a better picture of Middle Earth...but as authors who have tried to construct a world of their own have found out (like me!) doing so is haphazard at best. Right now I have TWO cardboard boxes full to the brim of tablets and notes of various ideas and scenes and notes that I have taken over the years...not to mention a LOT of blank books that are not so blank anymore because I have entered in information that I wanted to have on reference. If someone were to try to construct my world based on that, there would be inconsistencies too.
I think it important to keep 'canon' as it were...archaeologists refer to this as remaining 'in situ.' The context of something is not going to make sense outside the provenience it was originally settled.
But I also think it silly for the purists to get their noses out of joint when fanfic writers try to fill in the gaps or inconsistencies with ideas of their own.
Like the Took clan having stewardship ties with the Kings of Old...and Peregrin Took and Aragorn re-establishing that connection through Pippin's knighthood and the fact that the hobbit was strangely attracted to the Big Glass Ball that Knows All.