Final answer:
Thomas Jefferson was most troubled by religious interference (option b), as evidenced by his drafting of the Virginia Statute of Religious Freedom and opposition to the Alien and Sedition Acts.
Step-by-step explanation:
Based on Thomas Jefferson's writings, particularly regarding 'tyranny over the mind of man,' it is evident that religious interference was most troubling to him. This is underscored by the fact that Jefferson drafted the Virginia Statute of Religious Freedom, which was designed to separate church and state and ensure religious liberty.
Jefferson's opposition to the Alien and Sedition Acts and his support for the Kentucky and Virginia Resolutions further attest to his belief in limited government and the protection of civil liberties. His fervent defense of free thought and opposition to governmental overreach, especially regarding religion, informs us of his priorities and the principles he held most dear.