Quoting Wikipedia;
On May 12, 2008, the FBI and Department of Homeland Security agents raided the plant and arrested 389 workers who lacked documentation. At that time, it was the largest raid into a workplace in the United States.
On October 30, 2008, one day after the Iowa labor commissioner fined Agriprocessors $10 million for wage violations, Rubashkin was arrested on federal conspiracy charges of harboring illegal immigrants and aiding and abetting aggravated identity theft. Federal officials claimed that Rubashkin intentionally helped illegal workers obtain false documentation. After making an initial court appearance, he was released the same day on $1 million appearance bond after agreeing to wear an ankle monitor that tracks his movement, to limit his travel to northern Iowa, and to surrender his and his wife’s passports.
Considering these facts it’s unlikely that Trump will pardon him.