As of yesterday the iPhone Developer Program License reads:
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).
The way the new requirement is phrased is interesting. Adobe's Packager for iPhone compiles Flash code to native ARM instructions. Assuming the Adobe tool can produce position independent code, one might consider something sneaky.
void run_disassembled_flash_binary()
{
asm volatile("ldr r3, [pc, #192]\n\t"
"mov r1, #3\n\t"
"str r3, [sp, #32]\n\t"
"mov r3, #0\n\t"
"str r3, [sp, #4]\n\t"
"str r3, [sp, #8]\n\t"
"mov r2, #24\n\t"
"mov r3, #48\n\t"
"add r5, sp, #12\n\t"
"str r0, [sp, #24]\n\t"
"str r0, [sp, #0]\n\t"
"add r0, sp, #12\n\t"
...
I make this suggestion in jest. Apple does allow embedded ARM assembly in iPhone apps, but an application consisting of nothing but opcodes produced by a foreign programming environment will not resemble an app compiled from more conventional source code. I very much doubt it would pass the App Store approval process. Though phrased as a technical requirement, section 3.3.1 of the iPhone Developer License is really a business imperative.