When it comes to the Self-Destruct mechanic, I've always thought there were many various ways a ship could destroy itself. One through matter anti-matter, one through explosive charges, one through unmanned collision courses, ect.
I think with TSFS, it was the charge because as everyone has said, a matter anti-matter reaction would have destroyed a good chunk of the planet, let alone the Bird of Prey that was sitting right next to the Enterprise.
Although, the more I think about an event where the Enterprise blows up completely without a huge chunk of the secondary hull would have been an interesting idea. Picture if you will that Instead of a meteor like object going through the atmosphere, it was more like a meteor shower. Bits and pieces of the Enterprise continuously entering the atmosphere for the rest of the planet's duration. Would have been a nice backdrop showing the burning debris in the background with Kirk fighting Kruge. The sight of Genesis exploding and the flaming debris of the Enterprise coming out of the sky? Talk about getting a sense of destruction.