When a match setting is ffa, people want ffa. And no ´secret-diplomacy-team´ vs ffa.
Not at all! Look at the hugely successful diplomacy games, hugely successful zombie games and the Dreaming of World Domination (though this isn't a template as such - cheers for it though Mac and make another one!!!). All those examples enable private messaging and all were/are hugely successful. The best arguement I hear for allowing truces, alliances and so on is that these games are free for alls. Surely this means anything goes!
If you disagree with me, fine. You cannot complain here though. If you don't want this truces/alliances/pacts than state clearly in the game description "Truces are banned here." or something similar. Also, disable private messaging! This eliminates the possibility of someone making a pact without you hearing about it.