Is there a specific word for bacterial death?
Death is appropriate. Using this word to describe both unicellular and multicellular organisms places them in the same hierarchy. This hierarchy is the domain of life. 

Both prokaryotes and eukaryotes have unicellular and multicellular species. 

If you choose another word for death I would suggest not using it exclusively for bacteria. If a reader finds the idea of bacterial death esoteric, they may be inspired to dig deeper into the subject. Encouraging an informed reader would seem to be an effective device in a paper for communicating scientific information. 

You could qualify the word 'death' to be more precise. Senescence is the natural process of deterioration of life with age.  

Google has a great tool for tracking word popularity. Here's a Google graph for 'senescence'.