Crude has a higher energy coefficient as well.Crude is only efficient because we didn't have to make it, but everyone can agree that we should be figuring out ways to stop using it, not necessarily because of price (though that helps) but because it's really bad for the future of the planet. Biodiesel doesn't stand up as an obviously better alternative to regular diesel from an environmental standpoint, forgetting about costs and efficiency. Is it marginally better on paper than petroleum based diesel? yes. Should we be basing our national alternative energy policy on it? Definitely not.
So what should we do?
I think we should be at a level of self-sustained production. We only use what we can produce and go from there. If we outsource our energy needs, then we invite ourselves to other issues. As you stated, poor countries cutting rain forest for palm oil and stuff.
I know what Brazil does isn't perfect, but the idea is far better than ours. Having sugar cane based ethanol reduces the reliance on outsourced energy. Oregon has local soybean farmers supplying the B5 additive used in all city buses. Again, not perfect, but better than most.