So the hydrocarbons in the ground are not part of the ecosystem. How did they get isolated? They were once part of the living flora or fauna that got buried. In geologic time they were certainly part of the ecosystem. We, through their conversion, are bringing them back.
In the distant past CO2 levels have been orders of magnitude higher than today and yet life survived and we are all here.
Hydrocarbons like methane are found in distant heavenly bodies. How did they get there? Methane is a much more powerful green house gas than CO2 and there is a moon out there with a methane atmosphere.
Green house gases are part of the natural universe, and the atmospheric processes here on earth have adjusted to that without our intervention.
The chemical energy in petroleum collected from dead saltwater algae and was eventually entombed by Earth because bacteria hadn't yet evolved to eat all the dead algae. One way to reduce natural CO2 emissions is with antibacterials. About 4 ppm chlorine in the ocean water near the equator would shut down most plant food emissions.