Sure it will work.. lithium battery voltages sag a bit with load, getting you down to 3.5 volts or so. Brand new alkalines can have a voltage in the order of 1.6 to 1.7, so any well designed driver should be able to handle both a pair of alkalines and a single lithium cell.
The problem with many pen-style lasers is that they come with badly designed drivers: they work fine at 3 volts input, but as soon as the battery voltage starts to sag, so does the current to the laser diode. Lithium and NiZn cells have a much flatter discharge curve, and will work better.
NiCd and NiMH cells may also work, but they supply only 1.2 volts to begin with, so the driver needs to run properly from that. If it does, using rechargeables is often better than alkalines since their voltage will not sag that much with ongoing discharge.