Is there sin for one who stoned a cat with stones until it was no longer visible, or for one who threw a cat into a well to get rid of its harm?

There is no harm in killing harmful animals, but it is not permissible to torture them. Throwing cats into a well is not permissible and is against the Sharia (definition). This method is not a legitimate way to get rid of them, and there is no specific legal expiation for it except repentance. One should seek forgiveness for the grandfather and grandmother, or perform good deeds on their behalf.