Painting over the grass will just add to ground textures already there. In the Construction Set (and I believe the Geck as well), you could press "i" while in landscaping mode, if I recall correctly. This would bring up a window with a total of four quads for the cell you're editing, which holds all the current ground textures. You can delete it from there - with care, though.
Center over your cell and press b to turn on cell borders. Enter landscaping mode by pressing h. Refocus on the render window and press i. You get a list for the 4 quads in the cell showing the textures in use. Right click gives two options, one of which is delete. It doesn't work. The other option is replace. That does work.
To work out which quad is which in the cell, select Cell from the World menu and make sure it has your specific cell highlighted. There are check boxes to hide land in each quad and if you click apply, it will become apparent which is which.
Now you need to replace the landscape texture that is responsible for the grass with one that has none. You'll have to work out which is which yourself, but the ID should give it away. If you replace a texture with one that is already there, it will amalgamate the two and then one less texture will show in the list. You can revert back to a single texture if you want and then repaint the entire quads as you like.
There is a limit to the number of textures a quad can have. At least, that's the way it's always been before. So you'll probably want to remove some of them.
http://steamcommunity.com/profiles/76561198030818695/screenshot/524904249325675218?tab=public
There is one major pain with this. If you find a fix, let me know. Loading in game will show the result you wanted, but reloading in the CK will not. It will still show the grass. It's as if the CK get's it's data for grass from the esm only. This makes life difficult when it comes to judging the density and makeup of grass that you add back in.