Our understanding of the greenhouse effect dates back to the 19th century.
Section 202(a)(1) is pretty explicit that the law does not limit the pollutants under the low to those known to the legislative body[1]:
> The Administrator shall by regulation prescribe (and from time to time revise) in accordance with the provisions of this section, standards applicable to the emission of any air pollutant from any class or classes of new motor vehicles or new motor vehicle engines, which in his judgment cause, or contribute to, air pollution which may reasonably be anticipated to endanger public health or welfare.
Edit: In other words: even if we could show that Congress was unaware of CO2's effect on the environment, it simply doesn't matter. The Act empowers the EPA to identify and address the pollutants.
[1]: https://www.law.cornell.edu/uscode/text/42/7521