Sinclair needed the Vanitas name to be clean, and he also needed the public to look favorably at the company so that he wouldn't have an issue with trying to expand the company in the future. Right now, Mark's presence was like a poker card. There were those who loved Mark for all that he had done in the city, and there were also those who saw Mark as nothing but a murderer. How can they improve the company if the public sentiment was this vague?
Sinclair was a businessman, and he knew how important public sentiment and your image in the eyes of others was. The mere fact that Mark was willing to go out into the public as a vigilante without caring about what sort of message that would pass on to those who invested in his company proved to Sinclair that Mark did not have what it takes to oversee this company.