Edited: Sorry I misread your initial question, I thought this was about imported webservices in your mendix application. I suggest you create a ticket for a mechanism where you can create a soap fault.
Then the server throws the wrong kind of exceptions. If you throw a com.mendix.modules.webservices.WebserviceException the error will be progated properly to the client as SOAP fault. (the latest community commons release has a function for this).
So on the server side, publish a microflow, which just calls the microflow that does the real work, and set exception handling of that MF call to custom. In the custom handling throw again as WebserviceException and your internal server errors should be gone.