Remember, the X and Metroids are "natural" enemies. In Fusion, the SA-X was willing to die in order to destroy the Metroid lab and an X core willing to blow up BSL along itself. Later, a SA-X "saved" Samus from the Omega Metroid which in reality was just a self-preservation method.

"Since receiving the Metroid vaccine, Samus has begun to incorporate some properties of Metroids into her own genetic makeup. This allows her to absorb X parasites in their gelatinous form to replenish her supply of energy and missiles.

Stick to the low ground and fire charged beam shots directly at the SA-X to destroy it. Your beam must be fully charged to damage it. As it approaches, Space Jump over the SA-X to the other side of the floor while charging your beam, and release the shot when you land.

Chronologically speaking, SA-X is the second doppelgänger/clone of Samus Aran, with the first being Dark Samus.