I know what I’m about to say will be controversial, but isn’t just barely possible that “the pod” in “That Which Survives” is a reference to only one nacelle? In other words, perhaps only one pod/nacelle was sabotaged and therefore only one needed fixing (or jettisoning)?
That is a simple and therefore extremely tempting solution!

The sudden presence of single, central reactor in Season 3 of TOS has always been a bit of a pain after two years of dialogue pointing to all the action happening in the engine pods (AKA nacelles). I believe this episode and
Elaan of Troyius are the only examples of such a concept prior to TMP.
Hmm, let me think...
EOT's engineering crisis (once Scott quietly disarms the bomb he claimed he couldn't disarm) is thus:
SCOTT: I've got bad news, Captain. The entire dilithium crystal converter assembly is fused. No chance of repair. It's completely unusable.
KIRK: No chance of restoring warp drive?
SCOTT: Not without dilithium crystals. We can't even generate enough power to fire our weapons.
...
SCOTT: Our shields will hold for a few passes, but without the matter-antimatter reactor, we've no chance.
At first glance, he might be referring to a M/AM reactor nearby the Engine Room (and the nearby crystal housing would seem to confirm that). However, what if the only M/AM reactors are in the nacelles, and the Dilithium simply converts that power into a form usable by ships systems which includes not only phasers and shields but structural integrity field and inertial dampeners etc? Yes the ship could still technically engage warp drive but the crew
would all be stains on the back wall.
This particular setup where the nacelles are the source of all the ship's main power (AKA the aviation model) can be traced to numerous other episodes going back all the way to
Mudd's Women and cooberate the notion that the (di)lithium crystals do indeed perform this function.
How does it fair with the events in TWS? This is where most of the "central reactor" dialogue comes from, starting with Watkin's final mission:
SCOTT: Watkins, check the bypass valve on the matter/antimatter reaction chamber. Make sure it's not overheating.
WATKINS: But, Mister Scott, the board shows correct.
SCOTT: I didn't ask you to check the board, lad.
WATKINS: Yes, sir.
(he exits to an adjoining room and checks some controls there)
It might seem that Watkins is checking the reactor itself but all he's doing is looking at some panels. In fact (unlike the extremely dangerous transparent warp core in TNG) all control panels in TOS are remote from the source. Watkins' room therefore is probably just some sort of dedicated warp control suite.
However, then there's further dialogue like this:
SCOTT: I sent him in to check the matter-antimatter reactor.
...
SCOTT: The emergency bypass control of the matter-antimatter integrator is fused.
...
SPOCK: As I recall the pattern of our fuel flow, there is an access tube leading to the matter-antimatter reaction chamber.
SCOTT: There's a service crawlway, but it's not meant to be used while the integrator operates.
SPOCK: Still, it is there, and it might be possible to shut off the fuel at that point.
Lots of references (as with Watkins) to a singular set of equipment. However, if we assume that Scott had already narrowed down the problem with the ship to one of the nacelles (perhaps weakened during the 1,000 LY transport) then the references to a single unit all fall into place. And Scotty suddenly gets a much more dangerous mission in the nacelle itself, what a hero!
You know what
Tin_Man, count me in on your controversial theory
EDIT: The "ramping up" of the other nacelle to balance the overloading one is probably an automatic function, designed to balance out any engine inconsistencies that might occur during normal operations. With the override controls damaged, Scott's comment about "the engines running wild" is indeed true, even if only one nacelle is actually malfunctioning.
The "jettison pod" in TWS could refer to just the antimatter bottles, the entire nacelle or maybe just the aft portion of it - there are several portions of the nacelles that could be designed to break off in that way. Lots of food for thought!