So far, nothing too big, but there's more:
Apprantely, this episode of
Asahina Mikuru no Bouken Episode 00 contained in the DVD will be a 40-minutes long "Directors Cut Version".
Now, anyone who have volume 6 of the novel, I ask you to flip to page 93, and look for these lines:
「...さらに『朝比奈ミクルの冒険 ディレクターズカットバージョン』を新たに編集した上で、DVDに焼き直して売りさばこう、などとも主張し ており、現在俺と涙目の朝比奈さんとで必死に止めようとしているところだ」
("Furthermore, she's also proclaiming that we should recompile an 『Asahina Mikuru no Bouken Directors Cut Version』, burn them onto DVDs and then sell them. Right now, me and a teary-eyed Mikuru-san are in the process of deseperately trying to stop her with all our might.")
Kyon and Mikuru won out in the novel... But it looks like Super Director Haruhi is going to succeed in getting that directors cut edition out after all...
In a way, you can say that Kyoani has taken this whole "remaining loyal to the original story" thing to the extreme.