All perfect praise be to Allah the Lord of The Worlds. May His peace and blessings be upon our Prophet Mohammad and upon all his family and companions.
It isn`t permissible to bury two or more dead bodies in one grave save in case of necessity; namely there are too many dead people or the graveyard is too small. An-Nawawi (May Allah have mercy on him) said, "It isn`t permissible to bury two men or women in the same grave without a necessity." {Al-Majmou` Shareh Al-Mohathab, V.5: 284}. Moreover, "It isn`t permissible to bury two dead bodies in the same grave so long as the first hasn`t turned into soil except in case of necessity, in which case it is permissible to build and plant over this grave; of course after placing a layer of soil over it.
As for the grave of the man mentioned in the above question, there is no doubt that it has its sanctity. Therefore, it isn`t permissible to exhume it as it contains his bones and, as in our country, the bones of the dead decompose after hundreds of years. In addition, A’ishah (RAA) narrated that the Messenger of Allah (Peace be upon him) said: “Breaking a deceased body’s bones is exactly like breaking them when he is alive.” {Related by Abu Dawud}. Moreover, Allah the Almighty Says {What means}: " We have honoured the sons of Adam; provided them with transport on land and sea; given them for sustenance things good and pure; and conferred on them special favours, above a great part of our creation." {Al-Isra`, 70}. Part of this honour is keeping the grave of the dead intact and preserving the sanctity of its dweller.
Accordingly, the grave of the man mentioned in the above question shouldn`t have been exhumed and the woman shouldn`t have been buried over him. However, as she was buried three months ago, her body must have decomposed enormously. Therefore, it isn`t permissible to dig up this grave so as to preserve its sanctity.
An-Nawawi (May Allah have mercy on him) said: "The reliable opinion of our school (Shafie) is that if the body started decomposing, then it isn`t permissible to dig up the grave to avoid violating the sanctity of the dead." {Al-Majmou` Shareh Al-Mohathab, vol.5/pp. 299}. And Allah The Almighty Knows Best.