Rokkon shojo does indeed mean purification of the six roots of perception. By my current knowledge there is no other meaning to it.
The usage however that is most known to people is during mountain climbing, or as haikugirl.me phrases it
‘rokkon shojo’ is a common expression often repeated while climbing a mountain, especially Mount Fuji. ‘Rokkon’ (六根) means ‘six senses’ (i.e. seeing, hearing, smelling, tasting, touching and conciousness). ‘Shojo’ (清浄) means ‘purification’. So, the phrase refers to purifying your heart of all the bad stuff (desire, anger, fear, depression, etc.) that comes from what we take in via the six senses.
However this would not make a lot of sense in koutetsujou-no-kabaneri. The way ja.wikipedia describes it.
This is a phrase as referred to in Buddhism. Which would roughly translate to something like
Cut of your obsessions, refer to your heart in a pure state. Do not see what is unclean, do not ask, smell, taste or touch. Cut off your contact with the world in order not to feel.
This does fit the series a bit better. By killing of your emotions, it will make it easier to kill. This is something used in the modern day military as wel.
It also fits into the series given that
a monster cannot be defeated unless its heart, which is protected by a layer of iron, is pierced.
refer to your heart in a pure state which I believe can also be interpreted as
cutting of ones heart (please correct me if I am wrong) a fair pun of sorts.