What is the definitive ruling on offering prayers for the deceased (Salat al-Janazah) between graves, and how can one reconcile the action of Aisha -may Allah be pleased with her- with the Prophetic Hadith that warns against taking graves as places of worship?

Performing the funeral prayer (Salat al-Janazah) in graveyards is a matter of ijtihad (independent reasoning) about which scholars have differed. Our preferred view is that it is disliked (makrooh). As for the chamber of Aisha, may Allah be pleased with her, where the Prophet, peace and blessings be upon him, and Abu Bakr and Umar, may Allah be pleased with them, were buried, it was divided into two sections by a wall: one for the graves and the other for Aisha's residence.