I don't have a problem with the idea that 1701 bounced off the atmosphere of Genesis and its frame was recovered later, after the breakup of the planet.
I don't have TSfS on DVD and don't recall clearly, but is it ever stated that they established orbit over Genesis? I don't recall that being stated. If not, the ship should simply have passed through the atmosphere and back into space. There's certainly no impact shown or felt by the characters.
It was shown burning up in the lower atmosphere, close enough to the characters that they could see it as a distinct fireball:
http://movies.trekcore.com/gallery/albums/tsfs/ch8/tsfs0971.jpg
Let's assume that the widescreen image covers, say, 90 degrees of the camera's field of view. That would make the fireball about one degree wide (perpendicular to its direction of motion). The
Enterprise was about 150 meters wide, but the surrounding plasma ball would be somewhat wider; let's say 300 meters. In order for something 300 meters wide to have an
angular size of one degree, it would have to be about 17 kilometers away. The fireball is shown maybe 25 degrees above the horizon,
which would mean that it's maybe 7 km in altitude. That's only 23,000 feet, considerably less than the cruising altitude of a commercial airliner. For comparison, the space shuttle
Columbia was over 60 km in altitude when its disintegration began. If the ship has already descended from hundreds of km above the surface to less than ten, then there's no way it's getting back out into space.
As for why the characters didn't hear or feel a crash, odds are that the ship broke up in the atmosphere like
Columbia and didn't make a single large impact. Even if it miraculously held together, it would've travelled hundreds more kilometers before hitting, and it simply would've been beyond the range where the characters would've felt it.
I've played with this scenario using Orbiter a few times as part of a SNW story I never finished. The ship model lacks the shattered saucer so the drag's not accurate, but even passing the ship within 5 km or so of the surface, it's headed back into space without crashing. Considering the mass of the ship, the durability of the materials, and its speed, the Enterprise would act like any big meteoroid near miss-- big blazing fireball that loses some mass on the trip through, but by and large survive the experience.

Oh. Hmm, I should've read this part before I did all those measurements and calculations.

Still, I'm skeptical. How fast was the ship moving in your simulations, and how does that compare to its motion as depicted in the film? True, some poetic license should be allowed for, and I'm the last one to say that every FX shot should be taken literally. But it's a story point that they could see the fireball with the naked eye and watch it long enough to comment on it, so I'm assuming it happened more or less as shown.
As for the durability of the materials, I don't agree with your conclusion. However durable its materials may be, the ship is a hollow, irregular structure in shape, and that's going to create enormous unbalanced stresses. Especially with all those huge gaping holes allowing air inside -- it would be ripped to shreds.