I think that SWORD’s real purpose is to act as the “sword” that will cut off the corruption in the Marines and assist the Revolutionary Army in taking down the Tenryubito.
We know that the goal of the Revolutionary Army is only to take down the Tenryubito, not necessarily the Marines or World Government as a whole.
SWORD then consists of members of the Marines who are recruited based on a secret animosity towards the Tenryubito and will rise up to fight with the Revolutionary Army against CP-0 and Marines loyal to the Tenryubito when the time comes.
After the Tenryubito are successfully taken down then the top-ranking members of SWORD would take over command of the Marines in the organization’s highest-ranking positions, which can explain how Koby can achieve his dream by the end of the story and become an Admiral.
This would also make sense from a logistical standpoint as Dragon would need allies inside the Marines to get the layout of Marine bases and Mary Geoise, including key points to attack, as well as informants to keep tabs on the situation within the Marines.
This would also explain how the Revolutionary Army was able to successfully infiltrate Mary Geoise during the Levely without being noticed as they would have the inside knowledge of when and where to go to successfully get in.
*Theory by MrQuillava