Currently, Minecraft's weather engine causes lightning to strike at random, which, most of the time, is good news for your wooden house. However, this flies in the face of all of those park rangers that gave you an outdoors safety talk when you were a kid, since lightning will always strike the path of least resistance (in other words, the highest point on the terrain). In short, the lightning class should be modified to strike the highest block in a given chunk, be that a house or a mountain or a tower with a bunch of creepers on it...
The problem with this is, it is going for realism, but after the first lightning strike, another strike on the same high place would be incredibly unlikely. Either way, the path of least resistance doesn't mean elevation-wise. It will go wherever the charge is opposite to the charge in the sky. This can be anywhere, so random strikes are probably more realistic than this anyway.
I would suggest making high, non terrain blocks and taller trees attract lightning, but still with random lightning now and again.