Your question beings with a supposition...that the poem is more about the boy than the girls (despite the fact that most of the poem is actually about the girls.) This is a pretty safe premise to go with, though, as I think that it is correct.
Even though most of the poem is written about the girls it would seem (upon closer inspection) to be more about the boy. Here's why I think this is so:
"When the boy's head, full of raw torment, Longs for hazy dreams to swarm in white, Two charming older sisters come to his bed With slender fingers and silvery nails."
The focus of this stanza is on the boy, whose head is full of lice. Even though his sisters are mentioned, his problem is the focus.
"They sit him at a casement window, thrown Open on a mass of flowers basking in blue air, And run the fine, intimidating witchcraft Of their fingers through his dew-dank hair."
This stanza focuses more description on the sisters and the setting, though the boy is represented as it's his "dew-dank hair" they are running their fingers through. He is the object of their attention and therefore the object of this stanza.
Stanza 3: He listens to their diffident, sing-song breath, Smelling of elongated honey off the rose, Broken now and then by a hiss: saliva sucked Back from the lip, or a longing to be kissed.
This is an oddly erotic section of the poem...the boy is noticing the feminine qualities of his sisters, most poignantly the fact of their kissable lips. This stanza, again, focuses on the boy and the unconscious observations he's making about the desirability of his sisters.
stanza 4: He hears their dark eyelashes start in the sweet- Smelling silence and, through his grey listlessness, The crackle of small lice dying, beneath The imperious nails of their soft, electric fingers.
Again, the girls are in close proximity to him, doting over him, their fingers probing his hair and destroying the invaders. He is very in tune to his environment. He can even hear their beating eyelashes. The words are very "sensory"; electric, crackle, sweet smelling.
Stanza 5: "The wine of Torpor wells up in him then — Near on trance, a harmonica-sigh — And in their slow caress he feels The endless ebb and flow of a desire to cry."
This stanza, again, focuses on the boy and his feelings. He is overcome with emotions as the girls "work him over." A "torpor" is a state that's sort of a cross between a hibernation and catatonia. He's enraptured by the attention the girls are giving him.
So, there you have it. The poem, though it spends more time describing the girls, is really about the boy and his feelings toward them. Don't think of it as being too creepy, either, but more the boy approaching a crossover to manhood that the feminine attentions of the girls are "aggravating." His feelings are not explicit, they're more hidden, and notice the way his emotions are making him feel toward the end...he wants to cry. He is very confused by his feelings, it would seem, but this again shows how focused the poem is on the boy.
I think you need a closer look ophelius. It never said they were his sisters. It said that they were older sisters, meaning the two girls were sisters. This actually corrolates with the authors real life. He went and stayed with two sisters to avoid going back home to his mother. This actually makes it less creepy and make more sense. It confused me too the first time I read it, so I researched it.