It turns out both the software and the OpenGL renderer had the same problem. According to the spec, when SDL_SRCALPHA is set, the colorkey is ignored, so we just need to convert the colorkey into the alpha channel.

/*
 *  jumphack.h
 *  SDLiPhoneOS
 *
 */

#ifndef _jumphack_h
#define _jumphack_h

#include "setjmp.h"

/* see SDL_uikitevents.m for more info */

extern jmp_buf *jump_env();

#endif