As others have suggested, but not explicitly stated, the diode is basic input protection for an externally accessible input. I.e. the pin is likely on a connector which the user of this device drives.
On the other hand, if this control input is not external, the diode is likely not required unless it's being driven from a circuit that provides a negative voltage under normal operation (i.e. maybe its a negative going pulse like +/-5V square wave, or being driven by an AC coupled waveform). Protecting a transistor like this if negative voltages are not expected is probably pointless since something far worse has happened if your circuit is driving a negative voltage unexpectedly, and in which case the base resistor R1 likely provides enough protection anyway.
Just noticed you mentioned that a microcontroller drives the CONTROL input, so I'd say the diode is pointless, since you've got a much bigger problem if the microcontroller is driving a negative voltage.
Also just as you alluded, if the microcontroller is always driving the output then R2 is also pointless. However, in reset state many microcontrollers will tristate their outputs, and possibly enable pull-ups. The enabled pull-ups could cause a small current to flow in the base, multiply that by a couple hundred and that's the current that would flow through the transistor. This depends on the strength of the internal pull-ups (~50 - 100kOhm is typical).