There are actually three levels of interaction which are restricted during niddah.
Intercourse is prohibited by Torah law.
Affectionate physical contact, such as hugging and kissing, is also not permitted. According to some authorities this is a Torah prohibition; according to others it is d'rabbanan.
The harchakot are rabbinic enactments that modify the day-to-day interactions of the couple. This enables them to "switch modes" so that they can more easily avoid both intercourse and affectionate physical contact. The harchakot are applicable whenever a woman is niddah, even if there is no possibility of intercourse.
Unfortunately, people do not become immune to temptation when intercourse is forbidden, whether for halachic or medical reasons. The harchakot are intended specifically to prevent couples from forgetting themselves at a time when intercourse is prohibited by Torah law. Therefore, they remain in effect even when intercourse is medically proscribed.