3.3.1 is a section of the Terms of Use of developers seeking to use Apple's distribution channel. Apple isn't trying to make middle-ware-built iPhone apps illegal. It just doesn't want them on the app store. An important distinction between the car/part and printer/ink analogies.
Forcing Apple to repeal 3.3.1 doesn't allow offending software to be built and sold (as it already can be), it forces Apple to stock its shelves with it and thus take on users' expectations that Apple will support it (by making sure an OS update doesn't break hundreds of apps by running afoul of a popular middleware package).
Forcing Apple to repeal 3.3.1 doesn't allow offending software to be built and sold (as it already can be), it forces Apple to stock its shelves with it and thus take on users' expectations that Apple will support it (by making sure an OS update doesn't break hundreds of apps by running afoul of a popular middleware package).