User blog comment:Master Sima Yi/Assassins vs. Templars: "good vs. evil."/@comment-4944520-20120401191626/@comment-1153722-20120401192344

Minerva: "But guard against the cross, for there are many who will stand in your way."

The First Civilization supported Desmond, but it isn't explicitly stated they are against the Templars. We can't be absolutely certain.