Thanks everyone for your replies! The ellipse method is interesting, but how do you make sure the ellipse is properly aligned to the isometric grid? I can sort of eyeball it but is there a technique to ensure the perspective is correct?
I actually found a solution before this question was approved by mods. I ended up divided my two circles in half along the horizontal diameter (which exposed the two nodes along the perimeter). I then used the node tool to stretch out the space between the two semi-circles.
And finally I added a full circle to create the "top":
It's a little more work, but the circle is properly aligned to the isometric grid.