The answer to both your questions is
1. Saber DID realise but knew if she told shirou that he would be totally confused also he didnt need to know. In the fate series, saber dosent enter the church and show lots of hostility to kotomine.
2. Saber only destroyed the holy grail's physical form - no wish was granted all the mud and magma was what was contained in the holy grail - if you destroy a cup filled with water, wont the water overflow? Also gil was swallowed by the mud and came out to be born again into modern day world. Saber disappeard of her own accorc had she been swallowed by the mud or drank it, unlike gil, who is already insane,her pure majestic moe-tsun heart would be corrupted and she would become sadistic saber alter- whom i just love.
Those are your answers any other questions?