If we take the location of the x and y to indicate the positive directions, then this is a fucking left handed coordinate system. At that point all bets are off about "where pi is" because that notion is only with respect to a standardized coordinate convention. Do you move clockwise or CCW in a left handed coordinate system? At the end of the day it depends on your convention, I could choose any fucking basis I wanted and it wouldn't change the physics.
Your professor sounds like a cunt and is probably a mediocre physicist himself, but unfortunately you yourself are probably not experienced enough with basis invariance notions that you couldn't articulate properly why your convention is just as good as any, as long as one clearly specifies the coordinate system used.
For what it's worth, I would have called it pi and simply worked under the (y, x) coordinate system. (Hence y = r cos t, x = r sin t, and t increases CCW as usual.) It's much easier to just relabel the symbols x and y (they're just symbols, nothing more) than to use a convoluted left handed coordinate system. But I would also make it abundantly clear on my paper that this is the choice of coordinates I am using, in case the professor/grader is a cunt.