I agree with Zenfur (and SteelBlue?) that just having a factory that builds chicken units as if they were any other ZK factory is not very interesting. A playable chicken faction should retain the aesthetics of the chickens survival game but adapt and enhance it for competitive multiplayer.
Most of the units produced should be mindless and suicidal, just as they are in survival mode. The player should have limited control over them, able to select targets but not control movement (and perhaps have some constraints in target selection, like maybe only able to designate a certain number of targets at a time, not able to change targets rapidly, or whatever). There could be a resource or status that the chickens player has representing "control", where having a higher control level or spending more control points or whatever allows the player to issue more types of orders or a greater number of orders. With low control the units stream towards the closest enemy; with high control the player can designate targets, collect and hold units at rally points, coordinate movement, draw formations, and retreat.
Instead of having a factory that produces units one by one, the chickens player gets a roost, which produces multiple units of a single type in a burst (i.e. just like in survival mode). Multiple roosts all burst the same type of unit at once (i.e. just like in survival mode). The player makes a build queue similar to a factory; the queue can contain up to three types of units in whatever ratio the player wants. The roosts "build" the units using whatever resources the player has streaming or stored, but doesn't release them at first; then every ninety seconds all of the "built" units are released all at once, distributed among all the roosts. In other words, just like survival mode, but under the control of the player.
Since ZK is inherently a territory-control game, the chickens player should also be competing over territory. Roosts can serve to control territory and act as a combination of factory, defense tower, metal extractor, and energy generator. Roosts should produce metal based on their proximity to metal spots, so that they benefit from being built near metal spots but don't have to be built literally on metal spots. Roosts should produce a constant amount of energy regardless of location, like any other ZK power plant. Or perhaps roost energy generation decreases when roosts are too close to each other, so that the chickens player has to spread their roosts out for maximum efficiency. There would then be a trade-off when building near metal spots - building many roosts close to a given metal spot would increase metal production, but reduce energy production.
Chicken production should cost metal and energy; chicken special abilities like cloaking and shields should cost energy. Excess energy should produce additional metal, similar to overdrive, so that chickens can use an eco-heavy strategy to compensate for giving up territory, just like other players in ZK.
Maybe issuing orders costs energy as well? That could be a way to implement the limited unit control capability I described above.
The chickens player can spawn an arbitrary number of roosts and place them in arbitrary locations. Each new roost costs metal and energy to spawn. The cost increases with the new roost's distance from every existing roost; so, for example, a fourth roost that is 100 elmos from the first, 100 elmos from the second, and 250 elmos from the third would cost 450 metal and energy (times some proportional constant). Maybe it goes up with the square of the distance instead of linearly. Some appropriate function can be found, no doubt. The point is to make it possible, but costly, to spawn anywhere, and possible, but costly, to spawn as many roosts as desired, with costs increasing non-linearly so that the chickens player has an important and non-trivial decision to make when deciding whether and where to spawn additional roosts.
Unlike the rest of ZK, chickens could have a non-flat tech tree. Each roost generates a constant amount of tech points, and once the player has accumulated enough tech points a new tech tier is unlocked. This way the chickens player starts with Chickens and Pigeons, but works their way up to the more advanced units - again, just like the survival mode, but under the control of the chickens player. And similar to survival mode, if the chickens' opponents kill roosts then that will slow down the rate of tech advancement - but the chickens player can compensate by spawning more roosts, which will of course cost them metal and energy.
The Queen should be spawnable once enough tech points have been accumulated, but spawning the Queen should be a literal all-or-nothing game-ender. If the Queen is killed, the chickens player loses (i.e. all other chicken units and buildings are killed). So even if the Queen is ready to spawn, the chickens player may decide to keep her in reserve if he's not yet sure that she'll win the game for him.
I think this could be a fun faction to play, with interesting and meaningful choices (including unit micro! but at a cost!), with strategies and goals that fit into the ZK framework (take and hold territory, protect and improve productive capacity, destroy the enemy), and still preserving the basic character and aesthetic of the Chickens as a weird alien biological hive-mind of destruction and hate.
This would even work to have multiple chickens players fighting each other.