You have quite a few options to deal with the tripod patching or removal.
- By far the best way is to shoot the nadir area with the tripod removed out of the way. This can be done with a tilted tripod, hand held or a tripod with horizontal arm. Some manufacturers of Panoheads like Nodal Ninja offer a Nadir adapter.
- You could use the Easypano software patching feature.
- You can convert your panorama to cube faces and edit the nadir tripod area in Photoshop using a combination of the Clone and Healing tools. You might even use a combination of another shot or shots and mask and blend via layers.
- Programs like Pano2VR and Panotools PTEditor allow you to pan and zoom "any" area of the sphere and extract and area for correction before placing this corrected area back into place.
I'd suggest you try the cube faces first and move on from there trying out the different options until you find the workflow that suits you best.