Rife machines always work by killing bacteria, right?

Not necessarily. Rife said that his machines could "devitalise" bacteria, viruses and fungi. He was quite specific in using the word "devitalise" as opposed to "kill". He demonstrated that his machines could in fact kill, even literally explode some bacteria etc., and some modern machines have been demonstrated to do the same. However it would be wrong to say that this is the only way in which the machines have a beneficial health effect because nobody has been able to perform clinical tests with all bacteria etc.

Many researchers and experimenters have failed to demonstrate the actual "blowing up" of microorganisms, yet in many experiments, exposure to a Rife machine has retarded development of colonies of bacteria and has rendered the bacteria nonviable so that they die off in one way or another.

The machine may work in many different ways at the same time. It may stimulate the immune system for example. It might improve the flow of blood and lymph through tissues. It may work by changing proteins, DNA or other complex molecules in specific pathogens that affect their ability to reproduce or survive. There are many possibilities. It is the complexity of the reactions that has prevented a definitive mode of operation from being determined to date.

It is extremely likely that more than one mechanism is occurring at the same time which further complicates the effects.