Githyanki will steal your stuff, kill your friends, and maybe take you away to be made a slave and work for them.
Mind Flayers will twist your mind into an obedient servant, do horrific experiments on you and your loved ones, and plant a tadpole in your skull that will snuff out your soul and transform your body into one of them.
Githyanki are definitely evil, but they are more of a... Mundane, mortal kind of evil. No worse than the Drow or another of the billion slaver races in the Forgotten Realms. Mind flayers go beyond that and are closer to devils, demons, and hags in that their evil goes way beyond the limits of what a more mundane race is even capable of.
