This application also has to start and communicate with a second program, that accepts newline-terminated commands on stdin and responds on stdout.

This "one text line in" results in "text line out" seems perfect for a TCPIP client-server. Make the second program into a server. The GUI program should start the server (if not already started), which is a wrapper around program 2. Connect with TCP/IP to the server and send your line-in. You can then do a non-blocking read on the incoming socket.