Frankly, I'm at a point where I'm at a loss trying to figure out what your
"The Naked Time" - Where is the line of dialogue that established that blasting out of orbit was still an option? The context of the episode suggests that by the time they finally got into the engineering control room their orbit had deterioted so much, that only warp power could save them from crashing.
"The Doomsday Machine" - Fine, deflector shields might have been knocked out by the same hit that took out the main energizers but that wasn't the issue:
(Another blast from the machine.) Spock looks up at a monitor of his science station, get's up and goes to Lt. Palmer's station
SPOCK: Sir, deflector shields are gone.
PALMER: (to Spock) Sir, Deck seven reports power failure in main energisers. Implementing emergency procedures. (another hit) Severe casualties reported on decks three and four. Damage control party sealing off inner hull rupture.
Lt. Palmer's report could indicate the reason for their loss of deflector shields or a independent event.
SPOCK: It has ceased fire. We're being held in a tractor beam. We're being pulled inside, Commodore. You must veer off.
DECKER: Maintain phaser fire, helmsman.
SPOCK: We have lost warp power. If we don't break the tractor beam within sixty seconds, we never will.
This is the decisive part and information. Spock informs Decker they lost warp power. Where is the report, how does Spock know, especially where is the proof to pursuade Decker to veer off???
Decker is so pre-occupied with satisfying his Ahab Complex that Spock has to snap him out of it.
Lt. Palmer's audible report was "main energizer failure", the ship is now operating on battery power (it can still charge its phaser banks) but has been practically crippled
. Instead of giving a lengthy explanation Spock highlights their biggest handicap (as a result of the main energizer failure) he assumes Commodore Decker, an experienced starship commander, to understand: "We have lost warp power".
Decker snaps out of it and understands, but now argues like a little child:
DECKER: But don't you understand? We've got to destroy it!
SPOCK: That, sir, is illogical. It is suicide. Attempted suicide would be proof that you are psychologically unfit for command. If you don't veer off, I shall relieve you on that basis.
DECKER: Veer off.
SPOCK: Emergency impulse power. (The ship is on battery power as it had been in "Mudd's Women" so it's fair to assume that "emergency" and "auxiliary" are the same).