If an RNA has the same number of Cytosines as Guanines, consider it be neutral. If an RNA has fewer Cytosines than Guanines, reward it up to a certain point. I would say stop rewarding the structure at 25-50% fewer Cytosines than Guanines. If an RNA has more Cytosines than Guanines, penalize it. Penalize the RNA more severely as that ratio increases. That is, the penalty for 25% more C than G is less harsh than the penalty for 100% more C than G.
I’d also like to see this strategy operate in reverse, if possible- that is, reward the RNA for when C>G and penalize it for when G>C.