I cannot reproduce the errors with the ad usage you're describing, on my HTC Evo and on the emulator. The portrait mode works just fine with advertisement, InhibitSuspend or SwVideoMode does not affect it.
Could you please give me the .apk file of the example, which fails for you? Which device are you using? Does it have physical or on-screen Home/Back buttons?
I've removed the limitEventRate call for Froyo and newer phones, please tell me if it has any effect on the lag.
Also I've fixed the bug with StartupMenuButtonTimeout=0 still showing the config button.
To get Java environment, you can call SDL_ANDROID_JniEnv() - it's defined in SDL_android.h, I've removed it some time ago, and added back now (and I won't be removing it again, because it's got it's own header now).
I did not find any disadvantage for keeping debuggable="true" inside AndroidManifest.xml, the C compiler optimizes all the code anyway, and Java compiler does not do any optimizations, as far as I know. There is a flag --no-optimize to the DX compiler, however it's not used by the Android SDK. And the advantage is that you can debug your apk file