It's not uncommon for mature males to have their genitalia out, sometimes for several hours, it's problematic only if it never retracts and dries out.
Usually, males try to mate only when the females are in heat, so mating might not be the cause of it.
Separating them might in fact increase the problem, because he would see and smell the female without ever being able to reach her, which will lead to frustration. Besides, if your female has a joey in pouch, separating them will increase the risk of joey rejection, because normally both parents take care of the babies.