People are getting far too hung up on the idea of "canon" for these games. Lighten up, what we have here is a video game series that's meant to be funny and have each game tell an enjoyable story, a series which doesn't in the least take itself seriously. The canon between the first two games and second two is pointless, all four games tell decent stories in their own right and don't need to be put together. Plotholes and continuity breaks are part and parcel of most franchises that are jovial and there to give a good laugh for a few hours of the day.
Someone mentioned Red Dwarf: a perfect example where canon matters not at all; there's a vague storyline that holds everything together, its ridiculously full of plotholes (most of them intentional), but it doesn't matter. Each episode should really be treated as its own thing. Canon in it is ultimately inconsequential.
In any case, Curse of Monkey Island and Escape from Monkey Island are here to stay (and have been for ten years). I highly doubt that if Gilbert is ever intricately involved in another Monkey Island game that he will say "screw these works by my former collegues and friends, I'm making my own Monkey Island 3!" He might have if they were considered absolutely atrocious, but
they're not, they're decent Monkey Island games in their own right.
Just sit back and enjoy what we've got. Who cares that it might not tie itself up together as neatly as the works of Tolkien? It doesn't matter.