I have to say that some of your statements are not clear to me and appear to be conflicting.
If you have to do everything in the mcu, research if the mcu has buffers or DMA for the ADC. Also, unless you have confirmed it via experiments, don't bank on reaching the datasheet spec on adc speed.
If you allow the use of an external opamp - which will simplify things greatly for you, use an opamp to create a virtual ground and charge up a capacitor with the current to be measured - assuming it is reasonably small. You can then adc the voltage on the opamp's output. The beauty of this approach is that a) it doesn't require a fast adc; and b) it by definition measures the charge flowing into the capacitor (ie. current integrated over time).