Was it correct to refuse to write the sentence, "That humans and animals all came from one person," in the context of a scientific theory, and how can one deal with colleagues who believe that?

What you did by refraining from writing the aforementioned sentence is correct, as it contained an evil. You should be keen to invite your colleagues to Islam and introduce them to it with wisdom and good admonition, as Allah Almighty said: "Invite to the way of your Lord with wisdom and good instruction, and argue with them in a way that is best." [An-Nahl:125]. Know that guiding one man through you is better for you than red camels. Be patient with harm, for you will be rewarded for it.