I dunno, sounds like they were indemnifying him for anything he stole pre-aquisition. The "in memory" clause just means that they won't defend him for anything he went on to steal after signing the contract. Still looks pretty suspicious for Uber.
I do agree I wouldn't have called it "bad acts" if I was drafting, "Pre-Signing Actions" sounds much better :)
There are honest reasons for a clause like that--mostly because anyone who poaches a direct competitor's engineer to have them create a competitive product is risking a trade secret suit.
But the WaPo article doesn't mention any qualifying language. If I were trying to draft a contract to cover incidental mind secret leakage, I'd only cover indemnification as long as he used best efforts to avoid disclosure. Now maybe the full contract has something like that, I've only read a summary of it.