Well the reason for the rule is probably to protect players from injury. It's considered basic equipment and it needs to be on at all times. Of course if you shoot and the boot comes off, the goal will still count. And if a boot comes off and you're nowhere near the ball, there's really no point stopping play because he's nowhere near the action. Obviously if you get involved with the play (and kicking the ball is getting involved) then play has to be stopped.
I'm guessing that Fergie was going to say that there was nothing dangerous about tapping the ball 2 yards to another player. Realistically Evra wasn't going to get injured from it but I think getting involved with the play should rightly be off limits. And, more importantly, it is off limits so there's no point calling it controversial. It wasn't really a controversial call IMO.
The offside goal? As good as it was, you could moan about that. But not about the 3rd goal.