Well it can't be the wrong decision if you're okay with it!
But neither would it have been wrong for another DM to disallow the choice, especially if the DM's preferences on the matter were well known. It could be wrong for the DM to be a jerk about it but that is a separate layer to the issue.
Though it is pretty easy to reflavor a 3e "elf ninja" as "vicious trickster with magic in his veins" – a lot of the ki stuff can be cast as faerie (or not-faerie) magic. I think that'd be my angle, assuming I had a thing against elves (pretty sick of 'em) or ninjas (they're ok).
But neither would it have been wrong for another DM to disallow the choice, especially if the DM's preferences on the matter were well known. It could be wrong for the DM to be a jerk about it but that is a separate layer to the issue.
Though it is pretty easy to reflavor a 3e "elf ninja" as "vicious trickster with magic in his veins" – a lot of the ki stuff can be cast as faerie (or not-faerie) magic. I think that'd be my angle, assuming I had a thing against elves (pretty sick of 'em) or ninjas (they're ok).