Thornton wrote to John Clarkson on 23 November 1792, “I think you have saved our Colony”. Then, when he arrived in London, he was received (so he wrote to DuBois on l July 1793) “with every mark of affection and respect and in short the Directors in private made great Professions to me but took care never to mention in public the services I had rendered them”. Once again, as with Falconbridge, the Directors were concealing their real feelings. Clarkson's outgoing generosity had endeared him to the Nova Scotian settlers, but it alarmed Henry Thornton, a cautious banker. The Directors were uneasy about the promises he had made, and not without justification. He had, for instance, not knowing that the Company intended to levy quit-rents on the settlers’ land, solemnly promised them in Nova Scotia that they would never have to pay quit-rents – a promise that was to embitter relations between the directors and the settlers for the next seven years, and eventually drove some of them into armed rebellion in 1800.

Clarkson, for his part, was impatient with “their want of Method and their want of Exertion, with their strict adherence to nonsensical forms”, and told them so. As he wrote to DuBois, “Their general way of doing things is so disgusting that I really could not keep my Temper and very often flew out in abuse of their general plans”. When despatches arrived from Dawes and Macaulay contrasting the success of their own style of government by firmness with Clarkson's style of government by persuasion and promises, the Directors decided to be rid of him. They tried to get him to resign, but he refused “to be the first to relinquish an Employ wherein my Heart is and has been so deeply interested in its success”. So he was dismissed. Then, rather than do anything to bring public discredit on the Colony (“for it has many enemies in this country who would be rejoiced at having an opportunity of prejudicing the minds of the subscribers against it”), he at once left London and took up a new career in business in the country (BL, Add. MS 41263, Clarkson to Thornton, 5 May 1793; Clarkson to DuBois, 1 July 1793).