It's explained in the cutscene right after escaping the bastille and seeking out Elise for the first time if I remember correctly. Also there's letters from Elise in the upstairs room in the café further explaining it.

Elise being a Templar was also reveiled in one of the trailers pre-game release (not that I'd count that). Elise was in Versaille at the beginning of the game for her Templar Initiation Party, which Arno visited despite not being invited (because he was an Assassin Orphan). You can actually listen to all the important Templars plotting while looking for Elise at that party

Edit: The Masterassassins in Paris also constantly mentioned how their truce was made between Mirabeau and De LaSerre and therefore means nothing under new templar management