Although I think "Clay is deformed when pressed " is better than "Clay is deformed by being pressed", I would like to know whether the latter is grammatically correct and sounds natural.
There are two problems with your sentences 1) is that there is no reference to the state of the clay,usually only wet clay can be deformed; 2) deformation is usually used to describe a shape change which is not intended, e.g. "the body of the car was deformed in the accident collision".
Your first sentence
Clay is deformed when pressed
means that clay will change shape when an external source is applied.
Your second sentence might be better described as
Clay is molded by being pressed
since "molding" is an intended action to create a specific shape.
"Throwing" clay is usually though of as "molding" clay, not "deforming" clay.