The US has two parallel justice systems. One is civil, the other is criminal. The purpose of the civil justice system is to resolve disputes and amend harms. The purpose of the criminal system is to punish.

Shkreli was charged in the criminal system; Theranos was caught up in the civil system.

You can’t take a plea deal in the civil system because there’s nothing to plead to. You can only settle, which essentially means the parties to the dispute figured out an agreement without the help of the court.