Milo, I've been told by a senior member, not to prune until after the first flowers. As a test (and before I was told this), I did prune a few tomato plants and a few i left alone. As it turns out, the unpruned ones grew a bit faster. Once the plants start taking off and has bloomed then it's safe to prune.
I also had another tomatoe plant that I bought from lowes that was about 6" to start. After it had it's first bloom and 3 little tomatoes, I started pruning it agressively. Soon after it started dropping every new flower. I think I didn't have fertilizer so It was conserving energy towards growing. Since I've stop pruning it and starter fertilizing it, it has started growing rapidly and stopped dropping it's flowers. I've since gone back to pruning it but very lightly. Hope that helps.