Effie Trinket - The Hunger Games : Being the Capitol envoy to District 12, Effie goes through a very long process which leads her to fully reject the Capitol education and principles she harbours in the first book. Despite having a hard time adhering to the rebels (mostly since they bully her due to her past and her origins), her meeting with Katniss and Peeta - whom she supposedly guides through the Games and mundane life -  joined with her affection for them and Haymitch opens her eyes to the cruelty of the Hunger Games and the flaws of the government, that she will thus forsake.

Dana Scully - The X Files : Dana Scully is sent by the FBI to debunk Fox Mulder's work on the supernatural, due to her extensive education and rational, clever persona. Throughout the seasons, though many paranormal encounters fail to make her into a believer, her doubts start to ebb away along with her trust in the american institutions. Eventually, she'll become Mulder's touchstone and strongest ally in his quest for the truth, disregarding her supposed loyalty to any organisation.

Castiel - Supernatural : Castiel, an angel of lower standing, is sent to rescue Dean Winchester from Hell as the Divine plan commands it. At first, true to his nature, the angel is fully devoted to Heaven's will, which he will soon betray by joining the side of the Winchester Brothers. Gaining more and more humanity, he will then fully dedicate himself to the brothers, often killing members of the corrupt system Heaven turns out to be.   
In the end, having gained values that are his own through love and freedom of thought, he will defend the brothers with his life, and earn himself a place among the main characters of the show.

Characters who are tasked with reigning in the MC(s) and end up switching sides