I never thought I'd say this, but if the ship has so little in the way of redundant safety features that blowing a huge hole through the side of the ship and multiple decks is part of the standard plan, I would rather serve under Picard!
It's
NOT part of the standard plan. Blowing a hole that big only comes about since the standard options were sabotaged. The standard plan is for the emergency overload bypass to detect a failing megnetic containment, use its own magnetism to quickly shunt the free AM along the plasma conduits and into the nacelles, which will temporarily act as magnetic bottles, and blast those clear of the ship (much like dumping the warp core becomes later). I further assume once they were clear of the ship, they will try to bleed AM into space where it might disperse and be spread out enough so it will be relatively harmless and so the nacelles might be reacquired and reattached rather than vaporized. I also assume something similar about antimatter when dumping the warp core in
TNG or beyond - get it clear of the ship and then bleed the AM off into space so the warp core might be recovered later instead of totally blasting itself to smithereens. You may have more pure, stored AM still in containment in the AM Pods aboard, so you're gonna need that core back in one piece, or what's the point? (beyond survival and being stranded, I mean).
This is something I still don't understand with your setup (as opposed to outright fear, see above) - how on earth can antimatter get up to the nacelles in the manner you're describing? Antimatter in the TNG engine model needs to pass through the reaction chamber (and react with normal matter, getting converted into energy) before being channeled through a plasma conduit and up into the nacelles, which contain just the warp coils, components designed exclusively to utilize the reactant output of M/AM. Warp coils are not a storage medium. If you piped raw antimatter in there I imagine you would just end up with an exploded nacelle.
Plasma conduits and warp nacelles are not meant to be used as long-term storage for antimatter. But they have magnetic containment built into them as part of the their job to control and contain high energy plasma, which would be charged particles - they are just not as good as AM Pods with multiple redundancies and superconducting magnets, etc. where pure AM can be safely stored for long stretches of time, and they don't have redundancies built in for that, so this will only safely work for a short time.
This after all is why the Enterprise had no choice but to travel faster and faster in TWS - the antimatter was being pumped into the reactor at an ever increasing rate and if it wasn't converted into energy and shunted off into the nacelles, the reaction chamber would soon be filled with antimatter to the point of beyond its capacity! Super-fuelling the nacelles was actually the only option they had to begin with, even if it meant accelerating to unsafe speeds.
It seemed to me what was going to destroy the ship at that point in
TWS were those very unsafe speeds which would tear the ship apart due to loss of structural integrity, and once that happens, everything comes apart. It did not seem to me they were worried the M/AM integrator was going to explode. Maybe it would have, but if so, that probably would have occurred after the ship tore itself apart. Maybe they are deliberately, like you assume, forcing the ship to run away to give them more time, but if so, that isn't made clear. If anything, they wanted to slow it down and tried to do that. It could be automated systems decided that was the option to go with, but there's no evidence of that. So the idea one nacelle is out of control and a "governor" is having the other automatically keep pace lacks TOS dialogue foundation to put so much stock in it, IMO. Not that any proposed system has enough of that to make it definitive. I just am still unconvinced there is a reason to discount my proposal.
The way the events play out in the episode, the ship loses power long before the shielding between the matter and antimatter starts to degrade. And it's not just a regular power loss either; in Mudd's Women the ship was on batteries and there was plenty of Transporter activity going on. Yet in TSC Scotty says they can't even attempt a beamup, although they've been on battery power for a far shorter time.
I think it's actually a 2- pronged attack from the Excalbians - first deprive the ship of power (by unspecified means) and then create a situation where there's a ticking clock which forces the coportation of Kirk & Spock (the red-zone proximity of the M/AM).
The fact the god-like beings have their hands in the works allows such questions to be virtually ignored or written off as not a problem or as somehow inconsistent. The Excalbians are dampening the power so it can't be used - but the M/AM containment is still decaying, so in 4 hours - BOOM! Kirk often suggests things to Scotty, which the engineer has usually already considered and discounted as impossible or impractical, but sometimes Kirk has a good idea, and/or sometimes it just takes command authority to go ahead with a risky plan.
TSC is perhaps my primary reason for devising a means to jettison the AM via the nacelles (Kirk said those could be jettisoned, and the problem was with M/AM redline/containment issues). But it's a drastic solution, and even if you survive, you may be stranded in space, and far from home, so Scotty wouldn't do it until the last minute, and probably would prefer Kirk ordered it if communications were open.
) - how on earth can antimatter get up to the nacelles in the manner you're describing? Antimatter in the TNG engine model needs to pass through the reaction chamber (and react with normal matter, getting converted into energy) before being channelled through a plasma conduit and up into the nacelles, which contain just the warp coils, components designed exclusively to utilise the reactant output of M/AM. Warp coils are not a storage medium. If you piped raw antimatter in there I imagine you would just end up with an exploded nacelle. 
