They're pirates, so logically there's always the risk of betrayal and treason. Many marines have also showed disdain towards the Shichibukai - system (Smoker, Fujitora, I even think Akainu). So why do they skill keep it? Simple, if the kind of pirates the Shichibukai is comprised of are not with them, they are against them. I'm not keen (in fact I hate it) to start going on on tier levels, but taking a reasonable wide margin into consideration, admirals, Yonkou and the Shichibukai all belong into the same category.
If they would not have the SB - system or would abolish it, they would have to fight all the SB pirates. Fighters of that caliber are also exceedingly rare. So instead of trying to fight them all and running the risk of losing all their own great fighters, they just let pirates take each other out. In the case a Shichibukai is killed, they can just switch him with the one who killed him or another similar pirate, while their most trusted fighting force is unharmed.
They are also very useful when it comes down to situations like the War of the Best. Without the Shichibukai, it would have been hell of a lot harder for the Marines to achieve victory. That war is also a prime example of strong pirates taking each other out.
Abolishing the SB - system does not make the pirates of that caliber go away and most of them well screw around either way. This system at least allows to control them to a certain degree.
