Measuring Remaining Battery Life
The term for what you're trying to figure out is "state of charge". http://en.wikipedia.org/wiki/State_of_charge

The problem with looking at open circuit voltage is that it varies with respect to temperature. So you would need different cal curves if you application has a wide temperature range, and you would need to perform a temperature measurement.

It may also be misleading because it will sometimes rebound after a short period of time after the battery has been loaded. (depending on chemistry, temperature, etc). So unloading the battery and then checking to see the OC voltage could give you lower voltage than if you were to come back 10-minutes later and check again.

http://batteryuniversity.com/learn/article/how_to_measure_state_of_charge

Actually measuring how much current has flowed out of the battery is a more accurate approach. It's called coulomb counting. After rereading your OP it sounds like that is something you had in mind by pulsing current and counting the pulses. The problem is the cell voltage drops (which it will considerably in an alkaline cell) your current is going to drop across your load if you have a fixed load. So more or less, you need to actually measure the average current through your sense resistor for each pulse, and then sum all of those currents together. Either that or rig up a constant current load. But you'll still need to be mindful that the rated capacity in aH will vary W.R.T temperature.