OK, everyone, please download and try 3.3.8 release. Just change the version number in the download link.
Two configuration options to change, "Auto Reload on Change" to "Use Apache binary wrapper", set "Apache Binary Path" to where the Apache httpd is.
This should install the wrapper script automatically. If "Auto Reload on Change" set to "No" or "yes", the wrapper script will be removed during next restart.
You can also try building a new Apache binary, it should replace the Apache with the wrapper script automatically.
Also, 3.3.8 might be able to survive even without the wrapper script installed. cPanel may not able to kill it, but I am not 100% sure. Please give it a try as well.