Typically, when I tell a ship to "Eliminate," it does a rather good job going full rambo. Although you're requesting your ships to "Eliminate" a target, they still follow a variety of AI checks.
Things like the amount of flux or hard flux a ship has currently generated, plus the officer's personality (if the ship has an officer), can influence how aggressively a ship will commit to your command.
It can be frustrating if you're pursuing an enemy ship with long range pressure weapons because anytime a ship generates too much flux, they'll naturally back out of combat to recuperate. This is where having good point defense and your own long range pressure can help.
