There's a slight bug here as well. I also annoyed Z'Ant at some point (must have been talking to the Umpani spy) so I went to the Mt Gigas first, then back to Marten's Bluff and gave him the alliance note.
However, if you initiate conversation with Z'Ant AFTER you've given him the note, after he's come over all warm and friendly, he'll still produce the "you traitors!" speech and attack. I assume that's a slight bug.
krok