It seems the circle-generating algorithm isn’t the best. On almost any circle I draw with the circle tool, I tend to touch up the border anyway, so it hasn’t been a huge problem for me. A possible solution is to draw the circle 1 pixel bigger or smaller and shrink / stretch the straight parts of the circle.
For example, drawing a 15x15 circle gives you a nice rounded one, just select the bottom half and move it 1 pixel down, then select the right half and move it 1 pixel to the right. Fill in the gaps and you’ve got a non-hexagonal 16x16 circle. It’s not as smooth as it could be, but how often do you need to make 16x16 circles anyway? If it’s that often you can just copy the fixed shape and paste it.