It makes sense, in legal terms. O J Simpson was acquitted of murder but the victim's family was able to pursue him succesfully through the civil court on exactly the same accusation and, on the same principle, the FA could pursue Terry in the disciplinary proceedings.
It's interesting to note that lawyers themselves don't have this distinction in standards of proof. A barrister facing such a charge of misconduct would be tried by the professional body using the same high standard of proof used in a criminal trial. It's tempting to say that what had to be proved in the criminal case against Terry is subtly different as to fact, intent, and the effect on bystanders, from what is required in the FA proceedings, but, reading the report, it appears that the FA tribunal found facts contradict the findings in the criminal case.