The Aquila (eagle) was the Imperium's symbol from the beginning of the Crusade, I believe. It was a thundercloud with twin lightning-bolts before that, during the Unification Wars on Terra. Anyway, though, one of the first things a traitor would do is remove the coat-of-arms of his former masters.
Interesting, although I think, technically, the eagle was not the symbol of the Imperium until after the Battle of Terra. That said, this is based on a very old (original) understanding of Warhammer 40,000, and it seems to have been retconned by a lot of company illustrators and some lack of attention to detail on the part of art directors... or maybe I am way off base.