In any game, you need to scout. Plop your factory and queue at least a couple of your lightest, fastest units (even before constructors.)
A general rule that applies to every Zero-K game is that you should have some sort of combat unit built in your first minute, and you should be using it right away. Against any competitive player you will probably be seeing raiders in 1-2 minutes at most and you need to be ready for them. If you don't, there is probably some sort of rush on the way which makes scouting even more important.
Send them to look for your opponent. Gunships are not a normal start (if you see it some sort of cheese is on the way, either Revanant rush, blastwing spam, comm kidnap or comm drop), and if he's going to comm drop, he's going to building a Hercules. Your scouts might even show you he's already upgrading his commander. Comm drop is not really a rush strategy. The Hercules is expensive, and so is the metal (probably at least 2K worth) he'll be investing in upgrading his commander (he's not going to drop it at L1, it'll probably be at least L4 so he can have a second weapon or a special weapon).
The metal he spends doing this is metal he can't spend on taking control of the map. You should be doing this in any game. Zero K rewards early game aggression. If you just sit in your corner building a few metal extractors and energy, your opponent will take control of the map and have the resources to spend on buffing his commander. If on the other hand you are taking the fight to him and securing metal spots while doing so, he will not be able to pump his commander because he will be too busy spending resources trying to defend his own economy.
By playing aggressively and securing map control, you will have ample resources to deal with the commander any way you want. In the worst case scenario, a Stinger or two in your base with a bit of support should stop it in its tracks. Alternatively, most factories have anti-heavy specialists which will make the job much easier.
And once it's destroyed, it's a large gift of metal.