As I posted on the FSM forum, I understand the sentiment. Many of the edits are painfully obvious in the film even when they have the benefit of being covered in the mix. To recreate those edits would require even further editing to create something approaching a seamless listening experience. I don't think I'll bother making edits of other cues.
However, 2 1/2 Miles Down is a special case. The full, 10-minute cue is a solid listening experience, but doesn't seem to be a case of "what was intended". Playing the cue under the film makes it clear that it was either recorded to play under a different edit of the sequence--the hits in the music don't sync with the cuts or reveals and it's much longer than the sequence, continuing all the way until Rose calls Brock on the Keldysh--or it was always intended to be cut and edited into the film per Cameron's needs.
The cue is ethereal enough anyway that the slow fades and ghostly mixing of elements are far less noticeable than cues later in the film. I just like what Cameron did there, especially Sissel's vocals and the sustained strings from "Post".