Is it permissible to leave the excess meters of land — taken illegally — as they are, and donate their value to charity, after the owning company refused to settle the situation?

If the land is owned by the company and they have given you permission to leave the wall, then there is no blame upon you, and you are not required to give charity. However, if the company does not own the land, or owns it but has not given you permission, then it is not permissible for you to leave the wall, and you must remove it. The actions of others are not a consideration, because what is unlawful does not become permissible by widespread practice.