(Spoilers All)

“...but the gods hate kin-slayers, even when they kill unknowing".

A dabbing of pitch amongst the embers of Theon Turncloaks smoldering mental ruin. A page of evidence linked to an entire group of essays, Theon's journey evidently portrays the most harrowing caricature of any individual I've ever come across in Fiction. Bear with me as I provide evidence towards the fact that Theon Greyjoy is, in fact, a Kinslayer of whom is reaping that of which he has sown. The Old Gods and New both curse the Prince of Winterfell.

"Theon knew the mill. He had even tumbled the miller’s wife a time or two. There was nothing special about it, or her."

Or was there something about The Mill and the Millers Wife?

"...The night before, it had been the miller’s wife. Theon had forgotten her name, but he remembered her body, soft pillowy breasts and stretch marks on her belly, the way she clawed his back when he fucked her."

Stretchmarks are a recurring theme whenever the imagery of the Millers Wife is raised in Theons mind, is this to alert the reader or Theon himself to possible cues and clues? The age of the youngest Millers son in the equation most definitely coincides when you work out the differences, sure Theon would have to of fathered the youngest child at a (relatively) young age, but the possibility is more than conceivable. In fact, we see boys like Wex (age roughly 13) visiting whores, so why not Millers wives and Greyjoy royalty, seems as if it'd be an easy feat for a Prince of the Iron Islands?

"...the way she clawed his back when he fucked her."
This line here denotes to me a certain level of intimacy and confidence//comfort that 2 sexual partners (especially one being of high-birth) would attain over a long span of time, indicating a longer history of intimate times.

"...we dipped the heads in tar ... His own head was pounding. He (Theon) did not want to think about anything that had happened before he knew his name. There were things too hurtful to remember, thoughts almost as painful as Ramsay’s flaying knife..."

Theon knows, in some part of his psyche, he is completely aware that this younger Millers son is his own get. Theon equates the pain of the flaying knife as basically the threshold limit of pain, he literally begs appendages to be removed, just to end the pain.
Now - a thought as painful as a flaying knife is certainly of much more magnitude than the murder of 2 random kids caught between a Kraken and an Act of Misdirection. Theon pains to think about it so intensely, and yet there it is... Theon, Kinslayer, is (in some, perhaps auxiliary way) aware of what he has done... he even broaches the subject several times - very noticeably here, toward the end of ADWD, only to recoil at the last breath to muddy up the fact;

"...They were only miller’s sons, from the mill by the Acorn Water. “I had to have two heads, else they would have mocked me … laughed at me… they…"

And again - Theon stops thinking on the matter, completely derails himself to avoid too much pondering, he's beginning to remember that painful process of recalling just what he has done. Whom he has murdered... The Son he has slain.

The final revelation is either going to be implied in some more obvious way in the coming books, or rather via a self-confession//moment of clarity Theon encounters within his own minds eye.
Deluding himself at the thought of the subject, Theon is only working to temporarily staunch the slowly bleeding revelation of kinslaying, the act of which he has performed...an act of which the Gods are 'not finished' with him for, indeed - Ramsay is not finished with him, and who better to play envoy to the Gods' and their punishment than Ramsay Bolton.

Any thoughts, misgivings or other news is more than welcome. note that this is all just speculation in the end and may not be true - but I completely back this theory up and would love to introduce more evidence but you're probably better off reading the essay itself - there are so many more examples to justify this theory. Read the texts and see for yourself, Theon The Broken Prince - Turncloak, Murderer... Kinslayer. A more tragic portrait of shattered teeth, broken bones and missing parts there has never been.

Source - Winterfell Huis Clos - Part II - The hooded Man and the Kinslayer, available here;
http://branvras.free.fr/HuisClos/Kinslayer.html