Any recommended paper or protocols? Autoclaving seems like not a good way as it might detroy the cell walls and stuff-I need intact bacterial components.
Any particular reason you are set on killing by heat? Spores are notoriously difficult to kill. If death is what you are after, a sporicidal/bactericidal compound is superior. If you want to keep things intact, make sure you get rid of spores and use a bactericidal antimicrobial (or for instance azide) to kill cells.