I'm not really sure of what sort of penalty you are suggesting? What else can they do during the race other than give him a drive through? Time added on after the race? A fine?
The penalty was harsh, but only in the sense that the timing was downright unlucky, if I am not mistaken, he was handed the penalty before the safety car was announced? Somehow, I can't see half as many people claiming it was harsh if the safety car had not come out and he only lost one or two places. This detail for me is of vital importance in this discussion, its not that the stewards where intentionally vindictive and cruel towards Alonso, its just the timing of the penalty was unlucky. To compound things for Alonso fans, Hamiltons penalty 2 weeks ago was lucky (in the sense he didn't loose any positions), although funnily enough they both served equally harsh penalties (drive through) according to the book.
The fact that Kubica's car broke, has absolutely no relevance to the stewards as far as I can tell. As Scaff pointed out, an illegal overtake doesn't become legal because a car breaks down later in the race. Again, Alonso was sodding unlucky that Kubica's car did break down as he couldn't return a place to a car that is now parked in the garage, as such the stewards had no choice but to penalise him.
So really, Alonso fans have every right to be upset, things really conspired against him this race with regard to luck, what didn't conspire against him was the stewards, they did everything by the book and to be honest, I don't think it was an unfair punishment. Afterall, Alonso should have given the place back straight away, he should have known this, Ferrari should have known this. Okay, they were asking the stewards if they should and unfortunately for them, Kubica's car died during that conversation. I don't even see why there was a conversation to be had though, Ferrari can argue he was forced off track, but he hadn't completed the overtake, he was no more than side-by-side, the only reason he ended up ahead by the end of that corner, was because he cut the corner, and that, is an advantage gained by going off-track which ever way you cut it.