First, let me state my position. When I saw it live, I assumed it was helmet-to-helmet and figured a penalty and fine were both in order.  I continued to hold this opinion until I was able to review the replay for myself, frame by frame. You can do the same here:

Watch it

In realtime, pay particular attention to how fast everything happens. It is bang-bang, and the screencaps below prove it.

This first one is a screencap of Chris Carr (#25) tipping the ball away from Heath Miller. You can see Jameel McClain (#53) on the 30-yard line to the right of Miller. Notice the gameclock: 2:26

This next screencap is less than a second later. Notice the gameclock, which was still rolling, still says 2:26. It's also clear that the hit is shoulder-to-helmet, NOT helmet-to-helmet. McClain, who had been on the 30, still has one foot planted on the 30-yardline. The play was moving toward him at least as fast as he was moving toward it.

This is a close-up screencap from the slow motion. It clearly shows Carr tipping the ball away, as seen from afar in the cap above.

And here is the hit by McClain, clearly shoulder-to-helmet.

After seeing these pics and the replay, I became convinced the hit was not only not dirty, it wasn't even helmet-to-helmet, and, in fact, it was a textbook tackle attempt gone awry only because Heath Miller fell down. McClain had less than a second to react, which is not nearly enough time, and his target is clearly in the "strike zone", which shifted downward at the last moment due to Miller falling.

If somehow you're still not convinced, read what an expert in the field, former VP and Director of Officiating in the NFL Mike Pereira had to say.

Naturally, McClain is appealing his fine and Coach Harbaugh is supporting his player.

Most importantly, Heath Miller did not suffer a broken neck. Yes, the result of the play was terrible to watch, but that does not mean that what led to it was in any way wrong, malicious, or even preventable short of simply not playing football. As Pereira notes, the Merriwether hit on Heap was far more egregious, as it was helmet-to-helmet and launching, i.e. intentional. That is the kind of hit a player should be fined if not suspended for.