I don't believe an enemy with a peace marker has any bearing on its ability to subjugate. Even though they are at "peace" they are still your enemy, so they can still subjugate a tribe marker.
I couldn't find anything in the rules that states otherwise.
Edit: I was wrong. The rule says if the active enemy's square space is peace, then perform a culture attack instead.
I'm stupid, I totally misread the last line where it says explictly not to subjugate with the peace status. Thanks!