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.

For unexplained reasons, the Omega Metroid from Metroid Fusion attacked Samus despite the latter having Metroid DNA, whereas the other Metroids in the Restricted Area ignored her. This may be because the Metroids in the Restricted Area were preoccupied with the SA-X who admittedly was attacking them at the time.

So, go into Morph Ball form and stay near the corners, moving accordingly to avoid him. Occasionally he'll open his mouth to spit fireballs at you; quickly get out of Morph Ball form, run under him and shoot a few missiles inside his mouth to damage him. As you hurt him he'll gradually turn red.