Yeah, the last option would be the most prudent, but we have two unhappy Magical Girls with us. Bet Sayaka will stab the damn thing on principle.
Although, another body is just going to pop-up immediately after like how it usually goes.
Irregardless, this isn't actually surprising, when you think about it. After the utter disaster that was Isabeau and the barely averted disaster that was Tart, that Kyubey would definitely keep an eye out for any Irregular Witches that could think and grow. I suspect he might have lowkey been keeping an eye on Hirako's operations.