All perfect praise be to Allah, The Lord of The Worlds, and may His peace and blessings be upon our Prophet Mohammad and upon all his family and companions.
The prohibition is for the wine itself, not what contains it. Allah, The Almighty, says: "O ye who believe! Intoxicants and gambling, (dedication of) stones, and (divination by) arrows, are an abomination,- of Satan’s handwork: eschew such (abomination), that ye may prosperSatan’s plan is (but) to excite enmity and hatred between you, with intoxicants and gambling, and hinder you from the remembrance of Allah, and from prayer: will ye not then abstain?"{Al-Mai`dah/90-91}.
As regards empty wine bottles, there is no harm in cleaning and re-using them. And Allah knows best.