1mS isn't a problem but check the decay time of light from the LEDs, the phosphorescence and residual charge may still produce some luminance after 1mS. Beware of reaction time of an LDR if you are using one, they can be quite slow. If you are taking the reading with an ADC, turn the power off, wait 1mS then take the ADC reading and turn the power on again. Remember that many small ADC, especially ones in MCUs, have a sample and hold circuit so you can 'snapshot' the voltage and then let it do the digital conversion while the light is on again.
Brian.