I think its not wise to get 3 yields just for settling a city, it should have another condition in my opinion. It also isn't really that low faith, There is a period before science takes off that its low, but its very strong early and very strong late. Also the faith has a low opportunity cost that you need to factor. For example the 3 faith from markets sounds strong, but in a lot of situations I'd assert that just 1 faith per city contributes more to a religion.I don't think it's an issue to have a pantheon that gives you some edge, early while being light in faith but let's say it's a problem, the solution you submit will make wisdom bad, you will forced to get council early which can be hard with tradition and/or with some cities early and you will be slowed down. So what's the point to pick a low faith pantheon if it's not to have an edge somewhere else ?
After thinking about this more, I agree giving a yield to the council isn't a good solution, because it compares poorly to anccestor worship. I do think something should change though.