Yeah. Its not a great way to do it because you compromise diode life and risk instant death with lithium batteries and what not. You can do it though. I've rebuilt broken pulsars with SenKat's diode on multiple occasions.
Perhaps the 2AAA is too small. I've seen posts about the MiniMag Mod, either direct or using a resistor and capacitor. Could the circuitry from the LED model be useful? Or is there a better 2AA host commonly used?
You can run it direct from2xAAAs if you don't mind that you're overdriving it a bit. You can't just replace a regular 5mW pointer's diode though. The driver is probably made to only supply enough current for 5mW output, and if it is a voltage regulator the driver will likely burn up from the current of a SenKat diode.