The episode synopsis on the TF Wiki says "Both ships spin out of control, crashing on nearby Earth." Doesn't sound like Prime had much of a choice.

And just watching a quick clip on youtube, Prime's last words before the Ark crashes into Earth is "We're out of control" and he grabs the controls, presumably to try and take back control of the ship and steer away.

So ultimately, in this telling of the crash, Prime is as powerless as everyone else to stop The Ark crashing into Earth.

Is there a different telling somewhere? I'd be interested to read/watch it.