Regarding Hostelworld their business model is not around getting payments for the hostels. They aren't a payment gateway. They are basically an hostel directory, with some sugar on it (they also collect user reviews and have a booking management system for the hostels). The value that you pay for reservation is actually earned by these websites as commission. In other words: the down-payment is not part of the hostel earnings at all. In fact, if you cancel, in most cases they keep the initial fee and the hostel looses the booking without any earning.
Booking.com is a bit different as far as I know, but It's not 100% guaranteed that you actually pay the hostel through it. Even though full payment is available and even though you input your credit card. This will probably vary from hostel to hostel, but your credit card is collect and it may actually happen that you need to pay when arriving to the hostel. I once asked why and they told me at the hostel that they had access to my information but they didn't have any agreements with payment gateways.
Another option would be to contact the hostel directly to know if they provide any means of secure payment in advance. In any case be very careful. Don't give numbers over telephone line and assure yourself that whatever payment method alternative they give you is actually secure.