Someone had mentioned in passing that in Floriography lilies symbolized friendship, and that got me a bit curious about the possible symbolism of the lilies in Noir.
As it happens it is specifically Peruvian lilies that represent friendship. I dug a bit deeper and found the following snipets of information.
— "White lilies symbolize chastity and virtue – and were the symbol of the Virgin Mary’s purity and her role of Queen of the Angels.
— As the flowers most often associated with funerals, lilies symbolize that the soul of the departed has received restored innocence after death.
— Belladona lilies are apparently pink not white, and are referred to as "Naked Ladies" because the leaves die back in the summer leaving only the bare stalk and flower. They are found growing on Corsica. I haven't gone back and looked at the scene, but I think Mireille's had leaves in addition to being white.
If we look at the meanings, the simplest explanation is that they were chosen because the lily is a funerary flower, and
Belladonna because it's both a Latin epithet meaning beautiful lady and the name of a poisonous plant. The idea of innocence after death is an interesting meaning, and perhaps it could mean a different thing at the beginning than it does at the end.
At the beginning it's not unreasonable to assume that they might be tied to Mireille's sense of guilt over the death of the person in the graveyard. The innocence symbolized by the flower placed on the grave could represent an innocence unattainable, because the act can never be undone. Absolution is something the dead can never give to the living in life. Perhaps more apropos is that this is an innocence Mireille doesn't expect to gain in death.
Forgiveness and innocence aren't the same thing, but in this case I think they are tied together. Mireille places flowers on a grave to atone for a mistake she wishes she had never made. She wants to be forgiven, and perhaps by herself more than any other. She wants to recover an innocence lost. Echoes of Nazarov here. Kirika has some rough times in store too.
At the end of the show it might represent an innocence restored to the dead assassin. To clarify this a bit, what I mean is Mireille may have been absolving her of the crime of trying to murder her. Not that Mireille wasn't guilty of exactly the same thing of course.

Mireille, as one of the living, can give absolution to the deceased for wrongs done specifically to her, but in so doing she is granting the one thing she herself can never obtain from that particular graveyard. Mireille herself indicates she expects a fate no different than that of her fallen foe.
Just to be clear here, at no point am I using absolution in the sense of
ecclesiastical declaration of forgiveness of sins. This is just personal absolution, and something assassins probably don't expect from their victims.
Tossing the flowers violently in the air and seeing them scatter is something I don't have a good idea for; other than it might indicate the futility of seeking forgiveness from the dead, or of forgiving the dead, or just seeking the unattainable from those who have left their mortal coil behind.
As far as them being "Naked Ladies," while the image there is certainly a bit interesting I suspect that this isn't what they were going for, and besides there is that shower scene for that. With that said, the idea of the naked ladies in this case could be symbolic; the fabric of the lies they told each other at the start is pulled away, and they are both honest about who they are, and to who they are, at the end.
Of course if you follow that thought to it's conclusion that's some wicked foreshadowing.
As far as chastity and virtue... Mireille? Chastity sure, they are referred to as otome after all, but virtue? Not in the sense associated with lilies.