Communicate to them that this is not an appropriate forum for their arguments, but remember that it is possible for people to disagree constructively, even if they disagree everywhere.
So, when looking at these cases, ask yourself:
Is this argument/debate on-topic? Such arguments have a tendency to devolve away from the topic of a situation. If the argument in question does, then remove it, and let the users know that it isn't on-topic.
Is this argument/debate out-of-line? If it's too disruptive or generates significant noise, take moderative action, and let the users know the behavior isn't relevant.
If it's on-topic and not out-of-line, let it be. It's alright to keep.
If it is vaguely irritating, and grows to be too much of a site disturbance cumulatively, just send the users a message to let them know you'd like them to cool it. Be sure to send them the same message, and be sure not to implicate either one of them.