You could install it so it measures between the battery and the controller on the negative side. The capacitors in the controller will filter the switching spikes. If you really want to measure motor current, then you need to measure on the positive side as you mention, or use the hall current sensor.
One other problem is; as I recall, a 324 output can only pull down, not up. the output swing limitation you mention may be problematic also.
You might consider another common amp, like a TL082 (or TL081, or 84). Radio Shack used to sell these.
On the inputs, using a 100:1 divider gives you maximum sensitivity, but some amps aren't happy with going all the way to the negative rail.
If using a TL082, change the divider to 5:1, so the inputs to the amp never go below about 1v. This changes the sensitivity, but the amp will have plenty of gain.
Another nice feature of a TL082 is it's so slow that you might not need any input filtering. I used caps to ground on the inputs, but you might also just try a single cap from the output to the negative input on the amp to slow the response. Most controllers also have ramp up speed limiting, so a sudden change in throttle input won't cause a sudden change in output.
"One test is worth a thousand opinions"