If you want to understand why Rubashkin is (largely) getting a free pass from right-wing Orthodoxy, it is important to understand the right-wing Orthodox view on science.
Scientists and veterinarians have clearly stated that the animals shown on the PETA video suffered unnecessarily. Orthodox rabbis who have made statements on the Rubashkin-PETA issue have disagreed with them:
It's just like "a chicken running with its head cut off," said one prominent rabbi. Another repeatedly claims that the animals are just like a "drunk trying to stand" on wobbly legs, and we all know a drunk does not feel anything.
As several animal scientists have told me, the ignorance of simple biology needed to make these statements is overwhelming.
Here's a primer on science and right-wing Orthodoxy, courtesy of Da'as Hedyot.
As you read this post please remember that in rabbinic eyes, animals walking three minutes after shechita are insensate, do not feel and may very well already be dead.