Originally posted by Turnbull:
The "deleted scene" you refer to isn't really a deleted scene. It is an outtake of a scene that actually appeared later in GFIII (when Archbishop Gilday begs Michael to help rescue the Vatican Bank). It was included in the DVD collection simply to show that, at one time, it was considered as the opening scene of the film, instead of the eerie, decayed Tahoe boathouse.
Putting the Gilday/Michael scene first would also make the papal award look more like a quid pro quo.