Hi Sievep,
The reason you don't apply with the cruise line directly is basically the amount of work that goes into a "newhire" and also the different countries we hire from. Cruise lines basically hire from every country under the sun, and it is much easier for the newhires to go through a hiring partner.
For every newhire that joins a ship, they must have a passport, some type of physical, appropriate documentation for that cruise line, agreement to company policies, uniform, etc.. etc... There are also (understandably) quite a bit of questions from newhires about what life is like on ships. In our field we get asked by techs all the time if they should bring their tools, etc... Basically it's easier for the newhire to have a liaison or someone to "hold their hand" all the way to the ship if need be.