Except for two things in this case:
1) The navigational deflectors are specifically designed to PREVENT this sort of thing from happening and
Not really. IF they had no limitations on available power, and were always 100% effective, that would be true. But we know about the power draw requirements for the "navigational deflector" so we know that there are limits on just how much it can do.
I see this system as a "pressor beam" that changes the vector of small masses in the path of the ship so that they're no longer in the path of the ship under normal starflight. Think of it as a broom, in front of the ship, as an analogy.
A broom can work when you're looking at moving a few grains of sand. But ram it into a sand dune and it's useless.
That's a pretty clear analogy to what we're looking at here. It would serve no purpose whatsoever, in this situation, and would become overloaded a mere fraction of a percent of the way through the atmosphere.
2) At the speeds you're going, the "crush" event may require a handful of microseconds to complete. At FTL velocities, that's the amount of time it takes for a ship to travel from the upper atmosphere to several hundred kilometers below the crust, during which time the warp field is still active and still smashing through the atmosphere at a few hundred times the speed of light.
I wonder where you got the idea that there's a TIME factor here, as though "time" is the driving variable. It would not be.
Rather, the driving variable would be "impinged-upon mass." Either way you look at it.. "hypervelocity flow through the warp bubble" or "hypercompression due to mass accumulating in the warp bubble" it has nothing whatsoever to do with time, and has everything to do with the mass you're forcing into that bubble (through flying into it). The time it would take to intercept a given amount of mass will be a RESULT, not a driving variable. Do you see my point?
The mass density of atmosphere is much less than that of water or rock, of course, so the time in atmosphere might be more than it would be in water or rock, to be sure, but since both would occur in less time than it takes for a single neuron to fire, it hardly seems like it would make a meaningful difference.
The only real issue is "how close to the ground would the ship be when it's destroyed?" It could never really penetrate (intact) below the surface, but it might make it close to the surface.
The warp field imparts motion on anything that passes through it, which neccesarily means that for these few microseconds there's a mass of air and eventually solid rock being accelerated forward at about a hundred times the speed of light. Even if this crushes your ship in the process, it also crushes a column of material at such insanely high velocities that you might as well have struck the planet with thousand tons of antimatter.
Well, I'm not convinced that the scale of the explosion is necessarily remotely what you suggest, though MUCH of what you say is entirely reasonable.
Yes, the ship itself would be destroyed in an infinitesimally short period of time upon entering an atmosphere (ST IV notwithstanding), and might even still be intact until reaching the surface in some circumstances. But in any case, it WOULD be destroyed. The question is... what then?
The mass which made up the ship would continue to travel, albeit in a different state. Let's call it "debris" even though that's probably a misguiding term... most likely, this "debris" would be made up of dissociated elementary particles which would not be identifiable as any form of solid matter whatsoever at this point. It would still be mass, which is really my point.
Your argument assumes that the energy level of this debris mass carries energy according to conventional newtonian rules. But it seems unlikely to me that such newtonian rules would apply... otherwise, the ship could never accelerate to warp FTL speed in the first place! No, "warp drive" must be non-newtonian. In which case, your assumption of the energy impact of this is unreasonable.
Now, we know that ships which "drop out of warp" do seem to have some residual sublight velocity when they do so. This is not necessarily reasonable, from any scientific standpoint I can see, but it's something we know from on-screen evidence, so we have to accept it for the purpose of this conversation, don't we?
I get the impression that whatever the velocity of the ship in real-space was before entering warp is the same velocity it has upon exiting warp. And we know that conventional sublight velocity in the Trek work is limited to less than 0.75C, and generally less than 0.5C. (Feel free to refine those values as you wish, I'm just tossing out ballpark numbers).
Well, once the ship is destroyed, the "warp field" will collapse imminently, but will continue to exist for some short period of time after the ship is reduced to elementary particles within that field.
The likely result is that the warp field will behave as a "penetrator" while carrying along whatever mass it has collected (a small portion of which would be the original mass of the ship). But the more mass it picks up, the faster the field collapses as well.
Once the collected mass drops back into real space/time, THEN the energy of that mass would be delivered to the "target," in conventional newtonian terms.
It would still be a massive impact, make no mistake, but I think you're dramatically overestimating the degree of devastation to be seen.
According to your calculation, ramming a planet with a galaxy class would blow the entire planet apart, leaving only a nebula filled with gravel and vaporized stone. More likely, ramming a planet with a galaxy class would create a massive crater and leave a scorched region about the size of Oklahoma. (And might result in a "nuclear winter" condition, on an earthlike planet.)
It would still be a big deal. Just not as big of a deal as you seem to think it would be.