I think the tradition of "graciously accepting" an alliance offer stems from the ubiquious FIRST term of "gracious professionalism." One of the definitions for gracious is "marked by kindness and courtesy." (Yay Webster dictionary) So maybe it's not as bad as we think. It might imply "We are SO nice and courteous that we're going to accept/decline your offer," but it could also be more like, "We'd like the say in the kindest way that we accept/reject your offer." Partially, it's how statements are inferred, really.
No one seems to really look that deeply into the acceptance statements, anyways; as long as you say "yes" or "no" somehow without being TOO ridiculous. (But I could be wrong here; I don't mind a bit of creativity
).