I think this is a lot like the situation with oldschool Photoshop: for a long time, people pirated Photoshop, and Adobe really didn't care — didn't bother to do anything to make piracy the least bit challenging.
This was seemingly because they considered the amount of money they could make off of sales to individuals, to be relatively trivial next to the amount of money they could make off of corporate volume licensing; and they knew that corporations wouldn't be pirating Photoshop even if it was trivial (because corporations always have the thought of an acquisition-time assets audit on their minds.)
Apple likely thinks the same way about this education discount: all their material income comes from volume purchases or alternate distribution channels (e.g. cellular carriers for phones), or in-store sales; with online retail sales being a relatively-trivial fraction. So it doesn't really matter if they're "losing" part of their margin on these online retail sales.
(Or, if you think about it another way: this is essentially customer-driven price discrimination. Like coupons are for grocery stores. The discounted price is Apple's true price — the price that builds in a profit margin they're happy with. The higher price is pure gravy if they can convince people to part with it. They put the higher price front-and-center, and make the lower-priced offer a bit obscure. People "spending someone else's money" don't care about hunting for deals; they just want to get the thing and get out. So you can milk the gravy from them. People who hold their bank balance more dearly, hunt for the deal, and find it. Still fine; still made a profit from them!)