On a side note, I just realized that the scene with Kirk lying in his report actually gives Scotty more oomph. He just saw the captain lie with a straight face to Starfleet Command. Later on, Starfleet puts the torpedoes on board and Scotty protests because he can't get clearance to check them out. Scotty resigning was always about his principles, but this time it's because that's twice now where he can't trust his own captain with the truth, which makes Kirk accepting his resignation even more painful for both men (and thus Scotty's drunken rant in the bar would have more motivation, too).
In the final version, Scotty had plenty of reason already to maintain the high ground, but the deleted scene would have put a more personal reason to the resignation.