It's probably for stuff like this that they actually have a transporter operator.
It's only unexpected situations where the parameters have to be changed (swarm of bees, mugatos) that seem to really require a transporter operator. Although he or she might just be really adept at putting in the proper coordinates so as not to beam into a wall*, this seems more likely to be computerized than the executive decision "should bacterium x be put on the filter list, or is it a helpful species that allows the Alienites to digest their food?"
*They make hay about this, but there's obviously some kind of pushing mechanism to the transporter that pushes matter out of the way at the assembly point. Otherwise everyone would've died in the first episode from nitrogen narcosis, if not spontaneously combusted.