Will colouring mortar weaken it?
What is mortar doing on the roof????  you mean brick siding up to the roof or on the chimney? 

Regardless, adding  mortar dye will not weaken the mortar if used properly. I would bet a paycheck that the contractor forgot to add it and is covering his butt. A good contractor would have discussed any concerns with the customer before doing the work. To use a different colored mortar on a repair where visible, sounds pretty incompetent to me.