Suggestion 1 - provide a command line option to have the program print the header. That way, scripts can ask it to provide the header, if it hasn't been printed yet, or tell it to not bother, if it already has been handled. The calling script might even want one version in one situation, and the other in another.

Suggestion 2 - have the program return a text string to the calling cgi, rather than sending it to the remote client. That way the invoking cgi script can determine what happens. In an extreme case, you might merely want to know how many characters were used to represent the message.