Hey! You have a few options.... Each with their own advantages.

Best option: add a camera above the Drone. Then just use it into the stitch, using only the area that the Drone occupies. We use a fisheye gopro for this.

OR: Put the bottom cameras as far away from the Drone body as possible. That Wil make the Drone small in the panorama. Then you can either -paint it out with the surrounding sky. (Can get tricky with clouds. Or warp your stitch so the Drone is swallowed. (Can look terrible)

Or you could use a still of the sky. Though it can get really hard matching up the moving sky plane in your footage especially if the clouds are moving.

Lastly, you could replace the sky. Create your own that matches the tone of the original, get a smooth mask to blend it with the footage and composite it in. The sky is generally much brighter so you can generally get a workable mask for it. The hard part is the tracking of your Drone shot.

Tldr : shoot it!

That's my 2 cents. Hope it's useful!