How to properly render riverbanks and coastlines which possibly overlap?

I would like to extend the OSM carto style to render coastlines, riverbanks and other edges of water features with a line. This is quite easy to achieve by just adding another layer for ocean and water features which render lines on top of the polygon-fill layers.

This looks nice and works as expected, except for parts where the water areas join. In OSM this happens along rivers and when rivers meet coastlines. I thought about trying to make this work using a stylesheet alone, and it can almost be done by drawing the casing first like is done with lines, but not quite, there are still artifacts at the joins, and it's difficult to get the layer ordering right.

It seems like the best way would be to preprocess the data and produce another set of ways that really do represent banks. That means that if any natural=water/waterway=riverbank/natural=coastline overlap, just remove both ways.

Is this a sensible approach? What tool can I use to preprocess the data in this way?