Is a bad thought in Makkah or Madinah considered a sin that is recorded, and is this why the Salaf did not prolong their stay there? What is the ruling on negative thoughts that plague a disabled person, and how does Islam encourage marriage to disabled women?

Belief in divine decree (Qadaa and Qadar) is a fundamental pillar. A believer endures the calamities of fate, for there is good in them that he does not know. Such calamities may be a sign of Allah’s love for the afflicted and the greatness of their reward. Indeed, one may meet Allah without sin, and on the Day of Resurrection, those who enjoyed good health will wish they had the status of the afflicted. As for your assumption that you receive half the reward for praying while sitting, this is incorrect; rather, you will receive the full reward, Allah willing, because you are excused. The reduction in reward is for one who prays supererogatory (nafl) prayers while sitting, even though he is able to stand.