I read it as Decker
believed that ramming something down the machine's throat would kill it, based on zero percent scientific reasoning but one hundred percent utter insanity/depression/suicidal ideation brought about by the deaths of his pleading crew combined with feeling powerless and overwrought. He's wanting to kill himself. Nothing more. Indeed, it's only after when he plows his teensy tiny craft into the thing does anything get picked up on Enterprise's sensors and that Sulu he was paying attention because nobody else was. Witness:
[Constellation Auxiliary Control]
KIRK: Kirk to Enterprise. Why are you launching a shuttlecraft?
[Bridge]
SPOCK: Whoever it is, Captain, has no authorisation. Lieutenant, raise the shuttlecraft.
PALMER: Enterprise to shuttlecraft. Come in, shuttlecraft.
[Shuttlecraft]
PALMER [OC]: Enterprise to shuttlecraft. Come in, shuttlecraft. Come in, shuttlecraft.
DECKER: Shuttlecraft to Enterprise. Decker here.
[Bridge]
SPOCK: Commodore, I must insist that you return to the ship.
[Shuttlecraft]
DECKER: You said it yourself, Spock. There is no way to blast through the hull of that machine, so I'm going to take this thing right down its throat.
[Constellation Auxiliary Control]
KIRK: This is Kirk. Matt, you'll be killed.
[Shuttlecraft]
DECKER: I've been prepared for death ever since I, ever since I killed my crew.
[Constellation Auxiliary Control]
KIRK: No one expects you to die for an error in judgment.
[Shuttlecraft]
DECKER: The commander is responsible for the lives of his crew, and for their deaths. Well, I should have died with mine.
[Bridge]
SPOCK: You cannot succeed, Commodore. Your only logical alternative is to return to the ship.
[Constellation Auxiliary Control]
KIRK: Matt. Matt, listen to me. You can't throw your life away like this. Matt, you're a starship commander. That makes you a valuable commodity.
[Shuttlecraft]
KIRK [OC]: We need you, your experience, your judgment. Matt! (Decker turns off the intercom)
[Constellation Auxiliary Control]
KIRK: We're stronger with you than without you!
(The shuttlecraft enters the planet killer, and Decker dies in agony from the radiation.)
[Bridge]
SPOCK: He's gone. Constellation, come in, please.
[Constellation Auxiliary Control]
SPOCK [OC]: Captain Kirk, come in please.
KIRK: Kirk here.
[Bridge]
SPOCK: Sir, may I offer my condolences on the death of your friend. It is most regrettable.
[Constellation Auxiliary Control]
KIRK: It's regrettable that he died for nothing.
[Bridge]
SULU: Mister Spock, sensors indicate a minute drop in the machine's power emanations. Do you think the shuttlecraft explosion might have done some damage?
Kirk's pleading, which is spot on, is all for nought... and you know that if Kirk had belched out "Come back, let's just send it in on autopilot to justify this magical reasoning you've yet to tell us and note we still think you're not acting rationally" wouldn't have gone anywhere.
But it doesn't help that (a) it's
not Spock who points it out in the first place as it'd otherwise be as much his station, if not more than at Helm, to notice the
energy output drop, with immediately making a neat assumption in the way he otherwise rarely does... and - more importantly - (b) Sulu asking if the correlation is the likely cause is surely obvious due to the lack of qualifying surrounding circumstances. Or Sulu was just being rhetorical and nice so Spock could have all that glory (so it's two character assassinations for the price of one, woohoo! Two birds in the hand making a big goopy mess and all...)
A big thing whose maw is wider than a dozen starships and is capable of destroying planets whenever it gets the munchies. In turn, one tiny, warp-capable shuttlecraft results in a
minute drop in power yet large enough to make a guess with (which the story does recognize). It's ultimately pure luckoneum that blowing up a starship within it, at the right spot, not too much farther in compared to the teensy shuttle as well, destroyed it.
But those are nitpicks - my previous rating still stands, the story IS more than the sum of its parts and by a wide margin, one that could fit two dozen starships through!
.