At this point, the evidence would indicate biofuels are more helpful to local ecosystems than the alternatives. Common sense would back that up, just thinking about it, they should naturally be less detrimental because they're, well, natural. We need to embrace them and spend more time finding out though, as it could potentially be very beneficial to us in the long term.
Biofuels can harm local ecosystems with increased fertilizer use, but the overall benefits of a reduction in global carbon emissions outweighs the considerations. There is no reason why farmers for biofuels can use organic methods or simply grow crops native to the locale that don't require a lot of work such as switchgrass and algae to produce biofuels.