It would seem that a 24VDC power supply and a microcontroller power supply could be configured so that the grounds are connected. If this were possible, then you could just put your resistors between the low side of the power circuit and ground and then connect the high side of the resistors to the ADC on the microcontroller. Even 8 bits should give you the resolution you are asking for. If the isolation is definitely required, there are other (more expensive) solutions.
So far, there are two ways that I'm aware of to do this:
International Rectifier has some prepacked chips that can do this. They are generally used for higher voltage systems, but should give you the accuracy you specify.
Allegro Microsystems has prepackaged sensors which operate on this principal. (I am not sure if they go up to 100 amps.) Another option is to use a magnetoresistive current sensor. F W Bell and others offer these units.