Honestly, the answer is no, it wasn't. If I could trade one life for 4,000, I'd do the deal every time.
The thing is, 4,000 abortions still happened that day. And unless you've got a battle plan and the force in place to actually fight that war, you're just acting like you're fighting it. And ultimately, you accomplish nothing.
Rudolph didn't inspire a wave of abortion mill attacks that severely impacted the abortionists' ability to murder American children. He didn't accomplish anything but a symbolic gesture that will be used against the movement as a whole for years to come.
If we're going to go to war over this, it'd be wise to give ourselves a chance to win the thing. Rudolph didn't do that. Thus, it backfired on him and the movement.
I agree with your overall point, though. Ending this holocaust is worth dying and killing for. But a civilized society must adhere to the boundaries of war and peace times, or we're just terrorists. I will not dishonor the victims of this slaughter by advocating terrorism.