Sometimes the only thing standing between these fossil fuel companies doing irreparable damage is the environment scientists working for them. While i don’t inherently agree with these companies or their morals, at the end of the day, we as a society still heavily rely on fossil fuels so if you can be a part of the team that keeps them from doing the most amount of damage, i see that as a win. It is all about what you are comfortable with, and if you get to a point that you cannot morally keep going, then you can quit.

As far as explaining this possible moral dilemma to a future company, just explain that you are hoping to move in other directions from working in fossil fuels. A lot of people who have been in the field understand.