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I may not be understanding you correctly here, but you can disable PHP, XML and WebDirect though the 3 "Enable..." checkboxes in Admin Console > Web Publishing, tabs PHP, XML and FileMaker WebDirect. This still doesn't stop the engine running, it will just stop the publishing (e.g., no longer list any databases with the XML request).
Other than that, I can't seem to reproduce this issue in my 2-machine setup (same FileMaker Server and OS version as you). When I toggle WPE off, I no longer get a response via XML.