As your daughter has already been diagnosed to have a epidermal cyst, it has to be removed. Since the epidermal cyst arises from skin appendages, it has to be removed through a cut from the outside. Yes, there is going to be a scar no doubt.
Please consult a plastic surgeon for its removal so the car can be made as inconspicuous as possible and kept within skin creases if possible. As it is in the cheek area as you say, it is very difficult to camouflage the scar. Secondly as time goes by the scar will fade.
But as she is still a child as she grows older there are chances that the scar will stretch as she grows. But, that is a risk you have to take because now the cyst is small the scar is going to be smaller, if the cyst grows larger then the scar is going to be equally longer.
Though I fully understand you concern as a mother, I would suggest that you please go ahead with its removal and after the removal please consult your plastic surgeon for scar care treatment. LASER resurfacing is not advisable for the child according to me. Also for the fact that, as she grows the scar is going to change, so please do not do anything right now apart from the removal and local scar care as advised by your surgeon.
All the best to your daughter for the excision.