I think the Medusa scene was actually very good in terms of the story. It's a reminder that it's not just that some gods are "bad" and some are "good." They all are mixed in that respect, because nothing about them is supposed to represent morality.
I think the reason they might fight for their own gods is partially that they are just the children of those gods, and also because in some cases the alternative (i.e. Kronos) is worse. And they don't even always fight for the gods necessarily. The lightning thief arc is for their benefit, but SoM is for Grover and Camp, TC is largely for Annabeth, stuff like that. They mean to protect themselves and camp, and the gods are sometimes helpful and sometimes nuisances.