Could you skirt around it and just remark "there are no viruses for AmigaOS"

(Probably not literally true. But functionally true in the sense that they were likely transmitted via infected floppy disks, of which there'd be virtually none left in the wild in 2007)

It wasn't the AmigaOS running in the emulator that they were worried about, it was the Windows system running the emulator. (Not that the average IT auditor there could have understood the difference.)