I can't remember which issue exactly, but Iron Man hired the Crimson Dynamo to "try" to assassinate Tony Stark, a ploy which he used to get Peter Parker to speak on behalf of the Superhero Registration Act as Spiderman. It was convoluted and a very dangerous political/social move, but it worked.
I say, "Nay, the end does not justify the means", in this instance.
But also, Tony Stark wholly overreacted when Peter Parker said he was leaving the side of the gov't and the Superhero registrars (name?) and damn near killed Peter while stopping him from leaving.