Interesting idea!
There are a few trade-off scenarios we should work through. First, how high do you want the quadcopter to fly? Also, is the goal of the quadcopter to locate the animal(s) or simply report what was scanned during a flyby? (i.e., if a rancher wants to locate the position of an animal the quad would need to sweep the land until the animal was found; but, if you wanted to sample the population of a wildlife refuge, you might want to set a flight path and merely report which animals were present). Each scenario may have a trade-off based on the flight time available vs the distance needing to be scanned at once. So, to stay true to my previous examples, if you were locating an animal then you would need to sweep the land (much like a Roomba). The number of sweeps would need to be compared to the range of the RFID scanner.
With that said, I don't think you will have any credible choice other than using an active UHF RFID tag to extend the range. According to wikipeida, the range of an active UHF tag is 100 meters but that probably assumes that the reader is fixed and you need to have a mobile reader. It might be possible to create an array of fixed readers/antennas to create a long range mobile reader...
Thoughts anyone?