Of course arguing "what does it MEAN" can be fun too. Right now I've set this as "story canon" for what I am working on.
You will do what you feel is right, of course.
"Somehow the antimatter in the warp drive pods has been deactivated."
Nevertheless, the dialogue is abundantly clear that "something" happened to the antimatter and not
the containment it had been stored in.
TOS is full of strange wording or even euphemism. The "matter-antimatter integrator" mentioned in "That Which Survives" makes matter-antimatter reaction sound like nuclear fusion while it is instead annihilation
In a broader sense "deactivation" means that something ceases to function. The only function of onboard antimatter is to annihilate with normal matter. The moment the planet killer somehow reversed the spin of the antimatter particles (thus and probably turning these into normal matter) these ceased to function in a manner of speaking.
Another explanation could be that Scotty prepped Washburn to make technical reports to the captain in such a fashion that the captain (and the audience!) would understand and not be embarrassed by asking back "What do you [does it] mean rendered inert?"