Why not keep it simple while providing the best of both worlds? If the binaries conflict, rename the GTK one mtr-gtk, install the non-GTK binary as mtr-cli, and provide a symlink to mtr-cli named mtr (or to mtr-gtk if you want to preserve present behavior).
Double-compilation in the PKGBUILD might be ugly, but it's no uglier than a split package and it has the same effect. Of course I'm assuming that the compiled binaries are small enough to make including both negligible. Or split the package, but still install the binary for each with the aforementioned names.
