The Orlesian Empire was created by Kordillus Drakon to create an empire under worship of the Maker, and he established the Chantry from the Cult of the Maker that he followed. The Chantry of Andraste is so intertwined with Orlais that Loghain and Maric discussed dissolving it. I'm not certain what your point is in trying to insinuate that the two are completely distinct from one another when the history of Thedas proves otherwise, or even that the idea that templars would be stationed in an Orlesian town is somehow implausible.
Just because the Vatican is situated in Italy, that doesn't make the church and the italian state one and only being. Regardless of how close the Divine and the Emperor have worked in the past, that doesn't change the fact they are two completely distinct groups with different roles, jurisdiction, personnel, borders, etc and thus, an attack by Templars would not be an attack by the orlesian state.
If the elves attacked an orlesian town because Templars troops happened to be there, that would make them:
1-Stupid for picking a fight with both orlesian and Chantry armies.
2-Despicable for attacking innocent humans because they can't be bothered to make distinction between them.
3-The instigators of the Orlais-Dales war.