mirith:
The diode prevents the voltage from the input to the output from differing too much (You shouldn't put 5V across the output while have a floating or 0V input on the linear regulator).
I don't get this part. Are you concerned about having 5V on the battery while the charger doesn't have anything connected to the input side of the charging controller? I didn't check the charging chip datasheet, but I don't see a diode protecting its input even on Sparkfun circuits, so my assumption is it's either embedded or the IC has an high impedence on it's output line.
If your concern is about the regulator/step-up then the battery is connected to the its input and the Arduino to the output, I'll probably put a switch to turn it on/off, but that will disconnect the battery from the step-up circuit
