Probably for reasons of pacing -- Robert Wise went in and basically fine-tuned the cut to within an inch of its life for the Director's Edition, and this included making many, many trims to scenes that were already rather short in the theatrical cut (the Kirk's quarters argument among them).
This resulted in several rather inexplicable snips to existing scenes, such as Kirk's second, waspish, "Viewer off!!" in the crew Rec-deck scene, McCoy's "...Or a crew of a thousand, ten miles tall!" during the entry to V'Ger, etc.
All of these small moments added teaspoons of actual character to the movie, and for a film often criticized as being desperately in need of every drop of characterization it can get, these trims are utterly baffling, except perhaps if Wise was trying to make Kirk look like less of an asshole in that scene.
But I'd still rather have Asshole Kirk™ in that moment, honestly.