If you're looking for a general way to subtract the populations, use the following code (adjust to fit your script variables):
import ATK
ATK.setVerbosityLevel(10)
# When we compute the populations under verbosity 10, they are printed to the screen!
pop = calculateMullikenPopulation(scf)
# Majority and minority populations
maj_pops = pop._population()[0]
min_pops = pop._population()[1]
# Magnetic moments
moments = maj_pops-min_pops
print "Magnetic moments (in muB)"
print "="*25
for i in range(len(moments)):
print i,moments[i]
The code can be made a bit simpler, but this way it should be clear what's going on!