The new clause was almost certainly targeted directly at Adobe, whose popular, though arguably inefficient Flash plug-in has been locked out of Apple’s mobile platforms. A major feature of Adobe’s new Flash CS5 is the ability to package Flash projects as iPhone apps- a process which now goes against the iPhone Developer Agreement. As a result, apps created in this manner can (and will) be rejected from the App Store and Adobe just spent the last year or so of Flash R&D for nothing.
Well, the truth is, unlike Flash CS5, most of the aforementioned SDK’s produce 100% Objective-C code- they are more pre-compilers than true compilers. However, the vague wording of Section 3.3.1 could mean that if Apple ever wanted to pull the trigger, they would be well within their bounds to ban any or all of these third party iPhone SDK’s. Although there is something to be said about the added inefficiency and possible lack of UI uniformity of a translation layer, since they haven't done so already I find the possibility of Apple banning such tools outright unlikely. This was, after all, probably a specific jab at Adobe in Apple’s quest to make Flash obsolete. If Apple were to expressly ban all third party SDK's, however- from the standpoint of 99% of all iPhone developers, nothing will change. These tools are more for people coming from other development environments and those already used to XCode and Objective-C will continue to code as usual.
Despite the understandable optimism of the various SDK’s blogs- we may not get a true sense of the fallout until April 22- the deadline to agree to the new Terms of Service for an iPhone Developer Account. Even then, iPhone OS 4 is still in beta, and therefore subject to TOS changes until it is officially released in June.