Up to that point, I had only a fuzzy notion in my mind of what 0.33333... even was or how it was defined. But the professor helped clear this up for me: that "infinitely-repeating decimals" was actually just shorthand for a limit definition, i.e. "0.333..." is defined to be the limit as N approaches infinity of (3/10^1)+(3/10^2)+...+(3/10^N).
A "proof" that just plays a trick on people's logically inconsistent assumptions to derive a result isn't very satisfying. You're not really uncovering anything fundamental through that proof, just playing games.
Edit: what I mean to say is there are reasonable things "..." could mean such that .99... and .33... are both not equal to 1 and 1/3, respectively. But there are none for which one pair is equal and the other not, as you rightly point out. So all your proof does is show that the other person's viewpoint is inconsistent, but it doesn't give any evidence for one of the two consistent viewpoints over the other.
What slips people up is that ignoring everything but the total pie consumed (taking the limit) is embedded in the definition of real numbers.
There's an analogous story with rationals: Suppose x1 = 1, y1 = 3, x2 = 2, and y2 = 6. If we plot them, (x1, y1) and (x2, y2) are clearly different points, but x1/y1 "equals" x2/y2 because they lie on the same line through the origin. We decide that we don't need to know about those individual points.