I usually use loose sowing media so i can separate the seedling easier and transplant them all into small individual pot. But separating the crowd to smaller group like daisy said is good idea too.
Agree with you all. Dont kill the seedling from hybrid parents. At least till them show their final leaf colour and pattern. Weak seedling sometimes have nice pattern and colour. They grow slower than seedling which greener or plain green which have more chlorophyl.