Some cosmologies are clean, some have overlap. A messy cosmology with overlap can leave a lot of room for interesting edge cases and variations. It is about what you want in a game. I am fine with clean cosmologies (I've made plenty of my own). But I think the broader appeal a game has, like say D&D) the more you are going to want some overlap, some messiness, so a lot of different flavors can be found.
The beauty of this of course, if you don't have to remove anything. Everyone is free to make their own cosmology in their own campaign, to make their own setting and publish it. I think that is a better approach that saying evil gods should go because their roles is maybe similar to other entities in the setting.
I don't disagree, really. I think it's probably easier to remove something than write up something to add. Removing the gawds from my setting was the easiest way for me to come up with something I was happy with.