The Council apologized to Ahsoka in The Wrong Jedi, even though as far as I'm concerned, there is really nothing they could have done differently. Had they refused to turn Ahsoka over to the Republic, they would have appeared to be setting themselves above the law, since any citizen of the Republic would have been subject to a trial under the same circumstances. There is no reason the Council should give Ahsoka special treatment. However, that is exactly what they did in the Citadel arc. They had rules, but apparently the rules were for everyone but Ahsoka.