TOS enforcement stems from contract law. A principle of contract law says that a contract is binding on both parties if they agreed to it, but there must be SOME benefit to each party. A TOS between a website and its users clearly meets this threshold, but in this case agiletortoise didn't gain any benefit from the website -- he simply wrote a program that directed the user's browser to go there.
That being said, the best solution is the one that agiletortoise used: simply direct people to someplace less hostile, like Google, Bing, or Wikipedia, instead of Wolfram Alpha. Wolfram Alpha loses, everyone else wins.