The person who was mainly responsible for rejecting Hitler, Christian Griepenkerl, died in 1912 of natural causes and thus did not have a chance to regret anything.
Griepenkerl was born in Oldenburg in 1839 and went to to study with Carl Rahl in Vienna who was famous for monumental art and had designed various frescoes in Habsbrug holdings in Vienna (a lot of allegorical figures). This deeply influenced Griepenkerl, who specialized in painting historical art, especially the use of allegory inspired by antiquity in portraits. He, among others, was mainly responsible for the frescoes in the Vienna Opera House.
Due to his work in this field Griepenkerl became a professor at the Vienna Academy of Fine Arts in 1874. There he thought a whole generation of famous artists, among them Carl Moll, Richard Gerstl, and Egon Schiele. While some of his students would later decry some of his antiquated opinions about art, the general judgement of Griepenkerl was that the man knew what he was doing.
When Hitler applied it was him who in 1907 rejected him with the note "not sufficient, few heads" and again in 1908 with not even letting him draw. As I wrote above, Griepenkerl died in 1912 of natural causes thus never having the chance to comment ever upon Hitler again.
The Vienna Academy of Fine Arts continued to exist from 1938 to 1945 and still exists today.
After the Nazi take over of power in Austria in 1938 there were, of course, changes implemented in the school, the most notable one, a complete purge of all personnel and students that were Jewish or known to be politically anti-Nazi. Immediately after the so-called Anschluss in March 1938, the Vienna NSDAP put three new men in charge of the Academy, Ferdinand Andri, Wilhelm Dachauer and Alexander Popp. Interestingly enough all three of them were aesthetically and politically close to the Vienna Secessionist group and had in the past had personal ties to Klimt.
They immediately began a purge and in the first days after March 12 already 13 Jewish professors were let go from their posts (almost everybody working at the Academy was a state employee since the Academy was and still is a public university run by state employees). Furthermore, the trio (of which Popp later became chancellor of the school in 1941) prepared a manifesto about what was in store at the academy. The new program consisted mainly of pushing a more "German" style of art, cutting ties to previous more abstract art styles within the academy and place a larger emphasis on the monumental. It basically lead to what we today recognize as typical Nazi style of art being thought.
What is also interesting and has only been revealed by recent studies is that the Academy "lost" only 20% of its personnel and only 7% of its student to the Nazi purges. This means that by the time the Nazis took over in Austria, Nazism was already a rather present force within the academy, especially its students. In light of all this it is hardly surprising that the Academy retained its prestigious status and continue to move forward, albeit with a slight change in the art style that was taught as prominent.
In looking through the literature, I could not find any reference to Hitler's thoughts about the academy once it together with all of Austria had become part of the Third Reich.
Sources:
Verena Pawlowsky: Die Akademie der bildenden Künste Wien im Nationalsozialismus. Lehrende, Studierende und Verwaltungspersonal. Vienna 2015.
Oliver Rathkolb: Nationalsozialistische "Kultur"politik in Wien 1938-1945.