I really think you should take some steps to secure the software on disk to avoid modifications.
Something your virussoft team can do is make some obfusacator/packer which doesnt impede program execution in any way like most commercial protectors do, and you could use it on your other soft aswell to make it more secure against malware tampering.
Something a bit more difficult for the malware experts than PEcompact, UPX or AsPack.
on another note, you also sell public and private builds of this software for income. (but this suggestion belongs in another thread I know.) I do think it falls under security 
cheers