The option is there and I use it but the gnome-terminal-server is the only visible gnome-terminal process anyway.
From an xterm with no running gnome-terminal at start:
jens@fedora-aspire:~$ ps -eaf | grep terminal
jens 6381 6319 0 12:17 pts/1 00:00:00 grep --color=auto terminal
jens@fedora-aspire:~$ gnome-terminal --disable-factory -t 'Program Console' -x sleep 1234567
jens@fedora-aspire:~$ ps -eaf | grep terminal
jens 6388 1 1 12:18 ? 00:00:00 /usr/libexec/gnome-terminal-server
jens 6400 6319 0 12:18 pts/1 00:00:00 grep --color=auto terminal
jens@fedora-aspire:~$ ps x -o tty,pid,command | grep "sleep 1234567"
pts/2 6392 sleep 1234567
pts/1 6417 grep --color=auto sleep 1234567
The last command with the output piped to grep is similar to what we do to find our sleep-process, that's why the tty is determined correctly, but the pid returned by wxExecute is invalid.
Currently I use 3.8 (Fedoora 19).
On Fedora 20 with 3.10 I get the following message:
jens@localhost:~$ LC_ALL='C' gnome-terminal --disable-factory
Failed to parse arguments: Option "--disable-factory" is no longer supported in this version of gnome-terminal.
so the functionality might already be removed in 3.8, but the option is still there.
With 3.6 (Fedora 18) it works as expected.