Regarding the websites mentioned their business model is not around getting payments for the hostels. 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.
You can try booking.com, that also includes hostels. It's not 100% guaranteed though that full payment is available for all hostels (even though you input your credit card).
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.