There is some research suggesting hip, knee, and ankle alignment is a key to preventing ACL injuries. Landing on both feet equally with the knees in neutral (not too far in or out) may be crucial. Landing on the balls of the feet and rocking backward may be a good training tip. And as you suggested, using the right amount of hip and knee flexion when landing a jump could prevent ACL tears.
Like many things it may be best to look at this problem on a continuum. To the far left of the line is No Play/No Injury. That's not an option for the athlete. To the far right is Play Hard/Use Any Form. In between may lay the secret to success. Combining the right injury prevention strategies while still enhancing performance is the balance to seek.
As with every new skill, training and practice make a difference. Repeating a new skill over and over is more likely to incorporate it into the athlete's natural form. The athlete may not use perfect form during every play in the game but the chances of injury
may be less with overall improved technique.