/pokekill All Pokemons every 30mins

You need to ask this to the pixelmon team not the aternos team .
You can also use command block , a scoreboard for every tick in the game and once it is at 36000 tick (30 min) or above it output a redstone signal that activate your command and reset the timer . If you do that you need to put these command block at the spawn of your world so it works everywhere .
You can use Better Pixelmon Spawner from Lypaka but it needs more "popularity" , it has a Pixelmon ClearLag every 5 minutes (I think you can change the timer) . (I dont have the link yet because its not uploaded yet )