That's true. My impression is that this is more or less a rubber stamp and the head is acting on behalf of the president. I can't imagine someone getting elected to this position that wouldn't take marching orders from her appointee. It's a lot of power to give one person.
In that case I don't understand your objection; the president is an elected official, so if this department head is acting on behalf of the president, the argument that this was done by an unelected official is kinda irrelevant.