Actually unbolting and removing all the gubbins should be easy enough. You'll then need a good body shop to fabricate and weld in a steel panel and finish it off to look half decent, unless you're very good at metalwork and body repairs.
I would say a good body shop, - a mechanic could (like you) dismantle/remove it and the frame for a seamless? weld but that leaves you to get it to someone with a big hole in the roof. A body shop can do the lot in one go, dismantle, remove, weld in new metal with no leaks and refinish.
It won't be cheap though, and what do you do about the hole inside where the sunroof goes and there is no headlining ?
The headlining may be a problem. The whole sunroof assembly is pretty big so there's no way to remove it without removing the headlining, and on my 94 I did that to it was thin fabric that rips easily and can't easily be removed in some places. I covered the hole with some 3mm aluminium plate, bolted and sealed. I never got around to replacing the headlining and in winter would get frozen condensation dripping on me as it thawed, and it was noisier.
If you just want to avoid the possibility of leaks, I'd consider removing just the glass, and put an aluminium plate over the top to cover it.
If you want a plate the original contour you may find a section removed from a GX breaker and have a bodyshop graft it in. There may be models in other countries which don't have sunroofs so it might be prevalent to contact Nayab Akbar on FB forums.
Lorin, we are close to each other, and I know of a bodyshop/classic car restorer that takes on all types of work not too far away. I have no connection with him apart from being a very satisfied customer and he's always busy.
I have used him/his small team several times in the past with my mrs Civic and my 120, - my 120 is in there at the moment, quality work and I wouldnt go anywhere else.
If you would like contact info, PM me