According to this post on Daring Fireball a new iPhone SDK Agreement release in conjunction with the iPhone OS 4.0 announcement today specifically bans any iPhone application not implemented in C, C++ Objective-C or JavaScript. The clear impact here is to the wide array of programs written in languages other than those.
Is that your reading of the clause in the new agreement as well?
Update: Here is the clause as printed on Daring Fireball:
3.3.1 — Applications may only use Documented APIs in the manner prescribed by Apple and must not use or call any private APIs. Applications must be originally written in Objective-C, C, C++, or JavaScript as executed by the iPhone OS WebKit engine, and only code written in C, C++, and Objective-C may compile and directly link against the Documented APIs (e.g., Applications that link to Documented APIs through an intermediary translation or compatibility layer or tool are prohibited).
Apple has had a ban on interpreted languages on the iPhone for a while now, but yes, I suppose this makes the ban more clear and more precise. I imagine that yes, Apple is saying that if you use a language other than C, C++, Objective-C, or JavaScript, you run the risk of having your app rejected from the App Store on those grounds.