Branching inserts might be a way to go, if it were even feasible for such a substantial re-edit. The danger in having any actual alternate version is that if it's any good, there's the risk of it becoming THE standard version, a la TOUCH OF EVIL.

(On a parallel but relevant side note, I thought it was neat that when FAMILY GUY did their STAR WARS parody, they usurped the original Death Star explosion rather than the current modified one. Good for them.)