Unity is also based on Mono and with that being a sizable commercial product I imagine that this is an issue which we've not heard the end of yet.
Banning all apps that are not written in Obj-C/C++ would, in theory ban all Unity games also, of which there are a large number already in the app store.
This question has also been asked over on the Unity Answers site, and their official answer is:
"We just heard about the iPhone OS4.0
and the new Terms-Of-Service. While we
believe we are fully compliant with
these we are right now doing all we
can to get this verified by Apple. As
soon as we know precisely, we will of
course share that info with everybody.
Please hang tight while we get this
sussed out."
Be interesting to see what they get told by Apple.
The thing is, surely saying that an app has to be written in a certain language is a bit of a misnomer, as once the app is compiled down, it's always a native binary regardless how it's been built. My guess is that all they can look for is some kind of signature in the binary to detect what tool it was built with. A flawed approach.
EDIT: There is an interesting overview of the situation on this blog: monotouch now dead in the water what does apples new iphone developer agreement mean