Guild Marks are actually a neat concept to obtain more customization for you class so I find it kind of strange that you plan on getting rid of it with the next update. When it comes to the introduction of new jobs I felt that perhaps you could use your Guild marks to obtain special job abilities for those jobs rather then all at once or through leveling.
Also if you consider keeping the cap at 50, Guild Marks offer a way to obtain new abilities without having to lift the level cap or place them somewhere around 1-50. If you were to keep abilities as they are now and then add to what can be learned by a class it would help prevent newcommers being overwhelmed by a wide range of abilities and once they understand the basis of their class they would be able to invest Guild marks into the abilities that they feel fit their playstyle.
By just having it all be level based I think it takes away from the overall characterization that can be done with your character and it really takes away a part of depth that could've been expanded on greatly. I hope you might reconsider taking away Guild Marks and implement it ina manner that can work with the Job system as well as a means to obtain abilities that are always being added to the list of Guild mark abilities.