If the iqamah for Prayer is given during your Tawaf or Sa`i, then you should interrupt your Tawaf and pray with the imam, and then complete the Tawaf from where you left off. You do not have to repeat the Tawaf or repeat the circuit that you interrupted in order to pray.
In this regard, Sheikh Abdul-`Aziz ibn Baz, the late Mufti of Saudi Arabia, stated: If a person interrupts his Tawaf for a reason—such as one who has completed three circuits then the iqamah for Prayer is given, so he goes and prays and then comes back—he should start from where he left off, and he does not have to go back to the Black Stone; rather he should continue from where he was and complete his Tawaf. This is in contrast to the opinion of some scholars who say that he has to start at the Black Stone. The correct view is that he does not have to do that. The same applies if a bier is brought in and he offers the funeral prayer, or someone stops him and speaks to him, or there is overcrowding, and so on. In that case he should complete his Tawaf and there is nothing wrong with that.