I don't know enough about the chemisty and ecosystem impacts of this but from what I do know I can think of one possible reason, at least, while the EPA's position makes sense. If a certain volume of oiled water is processed by a machine that has reduced filtering standards -- essentially, only removing the bigger or easier to capture materials suspended in the water -- it may make it harder for later cleanup operations to further address the remaining pollutants that were released back into the water. Either because they become much harder to detect (harder to see/smell/taste, or react to chemical sensors) or become harder to "bind" with cleaning agents. In other words, while at a logic-only level the EPA position may appear stupid, it's possible that from a chemical & logistical standpoint it may not be.

Regardless, I think it's reasonable to expect BP to be moving heaven & earth to clean this shit up as fast as they possibly can, since they made the mess in the first place.