Rupert is PRESUMED innocent till found guilty.
I'd go with:
Rupert was the snatch thief that the police had been looking for the past two weeks.
No comma and that instead of whom. This is a good old fashioned restrictive clause. Presumably there are other snatch thieves out there that the police were either not looking for or who they had not been looking for for the past two weeks.
The other version assumes the police already knew Rupert was the snatch thief or that he was being sought by the police for some other matter. I'm assuming that the police were looking for the snatch thief and that all you are saying is that that snatch thief was, in fact, Rupert. And if you want to go all high-register I would pied-pipe that whom up front and say:
Rupert, for whom the police had been looking for the past two weeks, was the snatch thief.
If you want good old colloquial English, who is just fine in this context:
Rupert, who the police had been looking for for the past two weeks, was the snatch thief.
