The best counter to Zenith (or any superweapon really) is to not let them finish it. Until it is completed, it's useless, it's metal not spent on either units, defence, or economy. If you focus on building units (that counter what they have, of course), you might be able to push through their defences by the time it comes online, and take it out.
The Zenith itself has a special weakness in that if you manage to disable it (either stunning it or taking out the power generation) before it launches its meteors, it drops whatever meteors it has collected on the surrounding area, damaging it.
The second-best counter is a superweapon of your own. Though this would probably require scouting the superweapon before it is finished, so you have time to make your own.