Remove silicone stain from ceiling
I think that painting over the silicone is out just because it's a different surface to begin with.  Assuming you had a paint that would stick to it long-term, the paint in that spot will always have a different sheen.

Removal is the best option, and it may be a matter of trying options to see what will work best and damage the ceiling the least.  Chemicals that soften the silicone can make the job easier, but I think they would seep into the drywall and create similar issues for painting.

You say you are worried about scraping, but I think it may be a better option even if it means patching the area with spackling or similar if you gouge the drywall.  I would try very rough sand paper (below 80 grit, then maybe a brass wire brush, then a sharp scraper.

I admit that I have never tried to remove exactly what you are dealing with, so take this as one man's opinion.