Yeah stun bomb them to hell. With stun bomb production running and shoulder launchers installed you'll be able to blanket the whole map with stun damage, at least for a couple of missions but you don't need more. Motion scanners'll make sure you won't get easily surprised by the invisible units. Get some plasma-resistant armor. Don't trust the smoke fully as Star Gods can fly and spot you from above (units can see 4-5 tiles inside the smoke and it is difficult to make smoke screen that high). Don't use chemical weapons, though, they're useless against Star Gods. SGCs can be found on any missions that normal highest-level commanders appear.