Peter Cushing did not play The Doctor in those films. He played a human character named Dr. Who. The two movies were reimaginings of two William Hartnell stories, "The Daleks" and "The Dalek Invasion of Earth", and so do not fit into the continuity of the TV series because they retold stories that had already occurred. Plus there were fundamental changes made to other characters (Barbara is Dr. Who's second granddaughter in the first film, for example). But the biggest change being Dr. Who is human and "Who" is his actual surname.
So while Cushing is generally considered an honorary Doctor (he was actually signed to play Dr. Who again for a radio series that never went beyond a now-lost pilot episode in the late 1960s), his version of the character is not counted among the official Doctors any more so than Richard E. Grant's Doctor in "Scream of the Shalka" (webcast) or the various male (and female!) Doctors featured in Big Finish Production's Doctor Who Unbound series.
Attempts have been made to reconcile "Dr. Who" with the Whoniverse in the expanded franchise. The closest the TV series ever got was Steven Moffat has confirmed that he originally planned to establish in "The Day of the Doctor" that the Cushing movies exist as movies within the Whoniverse (posters from the films were to have been in UNIT's Black Archive), but they couldn't afford the rights to show the images. This scene was eventually included (and greatly expanded to include a scene where the Tenth and Eleventh Doctors watch the film and briefly adopt Dr. Who's mannerisms, as well as calling each other and themselves by the name) in "Day of the Doctor" (novelisation).