But didn't he note in the confrontation in the Defense Against the Dark Arts class that Harry had chosen Quirrell as his Wise Old Wizard?

"“Harry… you must realize that if you choose this man as your teacher and your friend, your first mentor, then one way or another you will lose him, and the manner in which you lose him may or may not allow you to ever get him back.”"

Dumbledore's comment in his note just don't seem congruent with this comment earlier on, and it's this comment and not the note which seems congruent with reality.