The scientists exploited Cole. It was essential that Cole die at the airport as it provided the memory of his older self being shot, which the Scientists manipulated for his mission, as the memory was recurrent as a dream that continued to develop providing him new investigative paths or possibilities as well as drawing him closer to Dr. Raily, a psychologist whose entire job is understanding her patient's pasts and psychology.
Dr. Raily's sympathies for Cole helped their relationship develop, which was key into pushing them toward the final discoveries at the airport. With Dr. Raily identifying Dr. Peters as the trigger man from her past interaction with him, Dr. Jones from the Future stepped in. The Scientists had no interest in stopping the viral outbreak but lied to Cole about that, evident by his comment "I can't save you, nobody can." They could have.
Instead the Scientists chose to allow the virus to spread and to study the outbreak patterns and develop an anti-virus that they would provide in the future, allowing them to be seen as heroes, allowing them to continue and possibly expand their power and governance over the underground society as they returned to the surface of the Earth. This technique was used for the plot of V for Vendetta ("Imagine you have a virus and only you have the cure.")
Meanwhile, Cole is truly an essential messiah. James Cole has the same initials as Jesus Christ. However, he would probably never be known as a messiah.