You can't buy weapons on eBay, either. CVS no longer sells cigarettes. Famously, K-Mart stopped selling ammo after Michael Moore went after them. That said, were Visa and MC to refuse to do business with anyone selling any kind of gun, it'd make the PayPal/Wikileaks embargo look minor.
You can absolutely still use a Visa branded debit card to purchase Bitcoin. This comparison is asinine, and I'd expect nothing less from the New York Times.