Or did you mean the FT before the DQ'd player was replaced? Duh.
I don't know of any case play that deals directly with this situation. I can see the merit in both ways of handling it. The kid took a merited FT, so you could say that was his FT -- made or missed -- and move on.
But that gets tricky if it's only a one-shot penalty. It makes more sense to say that the ball never became live and the official screwed up by allowing the shooter to have the ball. Disallow the basket if it's good. Get the sub in and then shoot the proper sequence for the FT(s).
I guess I go with (man, I hate to say this) the NCAAW interp.