well, I don't know about the bacteria, I am sure you are being honest and truthful, but I have seen growers using the condensation off their air conditioners for YEARS with no ill effects...
and if bacteria is the ONLY problem, then a simple boiling of the water would suffice...
however, I think the 'air conditioner water' I have heard others using is from window mounted units...
If you have a big pipe coming out of your house to the unit, then I confess, I have seen some pretty nasty stuff coming out of those...