Yes, the "cyano" does refer to the chemical functional group found in cyanide, but like all things, extrapolation of a little knowledge can result in a large misunderstanding. This functional group is toxic in its simplest form, but is rendered harmless when incorporated into the cyanoacrylate molecule. Think of it like how sodium metal and chlorine gas are highly corrosive, toxic compounds, but when they join together to make sodium chloride they become a necessary part of our biochemistry.
-Blast