The discussion that Captain Ramsey and Commander Hunter have about the Lipizzaner stallions seemed like a weird moment, until you go back and listen to what they're saying and realize that it's a perfect parallel to the situation. Both Ramsey and Hunter are correct in some aspects of the stallions that the other side didn't know, and both make mistakes that are either pointed out or ignored. Similarly, Ramsey and Hunter's actions were both right in some respects (Hunter being unwilling to launch without a confirmed message, Ramsey being right that the information he had was enough to justify the act) and wrong in others (Ramsey attempting to circumvent the launch protocol, Hunter for disobeying what seemed to be a lawful order). In the end, Ramsey's admission that the Lipizzaner's are from Spain seems to also indicate his admission that he was wrong to try and launch the missiles.
Fridge Logic: The decision to use an SSBN to knock down the rebel missile silos. The Tridents are pretty fast but it would have been far safer, easier, and probably quicker to just park a carrier battle group or three off the peninsula the moment the saber-rattling began...there was some warning between the rebel takeover and launch code compromise. Even a fleet of Akula attack subs would have had major difficulty penetrating that, and a flight of Tomahawks or an F18/A sortie would just as effectively destroy the silos with a lot less...fallout.
If we're dealing with freestanding missiles, this would be correct. If we're talking about hardened missile silos there's a pretty good chance that conventional bombs would be ineffective. When something is designed to survive anything short of a direct hit from a nuclear bomb, its not going to be knocked out by a standard bunker buster.
Stealth bomber loaded with a nuclear earth penetrator. Hardened sites as described above are precisely what this combo was intended for use on.