A standard D/A won't work since they require a digital word input not a variable pulse frequency.
You could use an up/down counter with separate clock inputs for the up and down such as a CD40193. You could count for a specific period of time (say 1 second) and then read the output, and reset the counter for the next read. This could be readily done with a single microprocessor also.
Alternately you could use two frequency to voltage converters, such as the LM2907/LM2917, and subtract their value with an op amp difference circuit to get the flow difference in volts.