Sure, but to retcon it like that takes away from the emotional resonance of that announcement in the film. I hate how death is so mutable in comics ...
Well, at least it would be faithful to the source material.
Setting the series as a prequel wouldn't limit story possibilities at all - quite the opposite. It would free them up to do anything they could reasonably want with a super-secret international high tech police/spy/whatever organization, without people continually wondering why the fuck the superheroes never show up and get involved in the goings-on.