I don't know that there's a definitive answer to this one. They've done a lot mucking with victory conditon bonuses/penalties over the past couple of patches and a lot of the experimentation that people have done comparing methods no longer are meaningful. My impression is that a good military victory is the way to go.
Then again, the latest 1.0406X builds are using a new scoring algorithm (which is expected to undergo more tweaks next week), and I don't think anyone has played with it enough to know what the current deal is. Truth is, both given the fact that the scoring basis for this game is far from finished and that games get rescored based on new algorithms, you should just play a good, strong game, win how you want, and not worry too much. That 5K game today might be a 1K game next month, and that 2K game today might be a 6K game two months from now.
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