If the focus were more on the politics that created and destroyed rapture, the breakthrough in the power-inducing drugs, etc and less on running around killing things (basically not be that awful DOOM movie), I don't see why they couldn't pull off a PG-13 rating.

Third sentence in the article:
" Verbinski's wanted to make the film R-rated and with a budget of $200 million."

From the get-go they were going for an R-rated film. The underwhelming finanical results of Watchmen actually led the studio away from taking the chance of such an expensive blockbuster film and wanted to PG13-ify it, to which Levine decided to give it the axe.

If you read the article, it explained why this film was cancel