How did "run over him" evolve to "run him over" over the last 50 years?

Solution 1:

Run him over and run over him have distinctly different nuances for me.

Run him over has clear and malicious intent (to damage with a vehicle)

Run over him, absurdly, admits the possibility that the incident may be for his own good/enjoyment, or at the very least an accident ... (a simple description of an action, without implied intent)

So, a 'bad guy' will try and run someone over. A 'good guy' may run over someone by mistake.

Solution 2:

I am very surprised that you never heard this idiom 50 years ago. The OED has references going back to this one from 1860: "A carriage..darted under the arch of the gateway, almost running him over."

Solution 3:

My suggestion is that it happened by association with other, similar verbs.

Mary knocked over the vase. Mary knocked it over.

Mary ran over the dog. Mary ran it over.

The word 'over' has different meanings in those two cases. However most people aren't linguists by nature. Most of us use language unthinkingly. If it 'sounds right' then we'll say it. The fact that a sequence of words may be illogical doesn't matter to most people as long as their friends can understand them.