You don't have to use Square's POS features to use Square as a payment method. Their apps let you just type in a dollar amount to charge. I know one store that uses Vend [1] for their POS and Square for their CC payments. The Vend app launches the Square app when the cashier presses the button to pay by CC, then you switch back to finish the sale.
Who said it was? And what's wrong with having a standalone CC terminal? That's how most very small businesses (food delivery, auto service, tables at shows/markets) still take credit cards. Their wireless terminals aren't "integrated" into anything else, it's just a swiper/PIN pad with a 3G modem, and Square is the modern version of that.
It's certainly prefereble to have your POS integrated with your payments system. Otherwise, there's no guarantee, for example, that the amount charged matches the POS total. In addition, it's much easier for employees to steal, and it simply takes longer.
1: http://www.vendhq.com/