Is it permissible to remove environmental protection systems from modern cars for the purpose of repair, knowing that this benefits car owners but harms the environment?

If disabling the system or leaving it optional for car owners, then there is no objection to fixing the defect and removing this system, especially if it benefits the car owner, such as alleviating the burden of difficult repairs or high spare parts prices. As long as the competent authorities have not prohibited this and have left the matter to car owners, then there is no sin upon you in disabling or removing it.