It's pretty unclear what you really try to do. You mention CLNF and all that and have a DLL but you talk like you would like to implement everything in LabVIEW.
My suspicion is that you still want to call UA_server_run(), but from LabVIEW and the bad news in that case is that you can't do what you try to do. LabVIEW is dataflow driven. While it allows to call C functions, it doesn't and can't implement the full C semantics. Once it passes control to the UA_server_run() function in the Call Library Node, this code executes on its own until it decides to return. But since LabVIEW is dataflow driven and doesn't know pointers like in C, you do not have access to the memory location the running boolean is stored at that you pass to the function. If you branch the wire, LabVIEW will very "helpfully" create a seperate copy of that variable, not just pass a pointer around, since passing pointers around would completely go against the entire dataflow paradigm.
You will have to create a wrapper DLL that implements and exports the stopHandler() function as well as a function that calls UA_server_run(), passing it the DLL global "running".