Not an expert but have appied H1B stamp in BJ before...

I think you should wither stay here with your wife or go back together with her to apply for H1/H4 visa stamp in Beijing.

- Your h1B and Your wife's H4 won't start to take effect until 10/1. Why would it matter if she goes out of US before that? Your #3 does not make sense. You should check with your attorney.

- Rejection of H1/H4 visa is not very likely, just make sure you have I-797 approval as well as other suporting docs with you

- security check: not sure. This may be the only negative aspect