I know you don't want to hear it, but sodium thiosulfate is perfectly safe for microbes and many other incredibly delicate living things, it's what is still used in public aquariums small and large, and is incredibly cheap, especially if you mix it down to the OTC levels of 1%-3%.
While aeration is perfectly suitable for removing chlorine, it will do nothing for chloramine, you will need something that either bonds to it (carbon?) or breaks the bond between the chlorine and ammonia. Again, sodium thiosulfate is absolutely suitable and acceptable for this purpose.
In terms of water treatment, chloramines are actually preferable over chlorine, as chlorine has been linked to causing some cancers. The EPA has recommended that all U.S. water municipalities switch their treatment from chlorine to chloramine, and the specific purpose is to kill microbes. So, yes, it will (and should if it's properly treated water) be killing soil microbes.
I see that someone has mentioned using sugar, and while it's not something I have ever done, if it works, I say go with it. Not as cheap as sodium thiosulfate, but hey, it sure is easier to get! However, if you're of a mind, you can get it for something like $5 for 2lbs dry (which then needs to be mixed down to that low percent solution mentioned above). At the Long Beach Aquarium we would just sprinkle it in, used our noses to tell us whether or not the chlorine was gone. Chlorine bleach is used to clean many items, such as tank decorations, and that needs to be neutralized quickly.
