Let's take an analogy:

You're writing a video game that will run on hardware that doesn't do floating-point arithmetic (like the Nintendo DS), so you have to write a library to emulate floating-point arithmetic. You then port the game to a very similar system whose hardware does handle floats, so you replace your library with simple operations.

Mary's situation is similar: Mary is perfectly capable of anticipating any experience related to color, and "seeing red" doesn't change that, but allows her to use the functionality built in her hardware much more efficiently, replacing costly and slow verbal reasoning. So Mary's functionality hasn't changed - she's been refactored, and is reacting to that.

Another approach: the color-perceiving hardware in Mary's reacts to encountering new experiences by releasing chemicals / stimulating parts of the brain that corresponds to the subjective experience of "learning", hence her "Oh" of surprise, etc. The fact that she abstractly knows enough about that hardware to emulate it doesn't mean it won't react that way - it has never seen red before. Or in other words, part of Mary's brain is learning, so Mary experiences learning, even though if you consider her as a whole she hasn't aquired any new functionality.

So, your answer to "has Mary aquired new knowledge" depends on what you mean exactly, as it does for the tree falling in the forest:

• Has Mary's map of the world changed ? Has her anticipation of future events changed ? No.

• Has Mary subjectively experienced learning? Yes.

• Did Mary become better at thinking about color? Yes.