To the best of my knowledge the (in-universe) explanation for why the Klingons didn't have cranial ridges in TOS was because of a genetic disease caused by attempts to manipulate Klingon DNA to create augments (like Khan):
In the year 2154, the Klingons gained access to the genetic material of Human Augments and tried to adapt this genetic engineering to improve themselves.... One of the subjects suffered from the Levodian flu, which was modified by the Augment DNA to become a fatal, airborne, mutagenic plague that spread rampantly through the Empire, from world to world. In the first stage of this plague, Klingons lost the ridges on their foreheads
However, I recall seeing in the episode chain of Enterprise where the Klingons became infected with the virus, that the augmented children that the Klingons based their research on were augments from Khan's folk.
The scientist who leads the augments is Dr. Arik Soong (an ancestor of Dr. Noonian Soong, Data's father). Now if these children were augments then, in the prime timeline, Dr. Arik Soong likely found them aboard the Botany Bay and took them for safe keeping. However in the Abramsverse the Augments are likely under section 31's control and so would be kept under guard on earth, meaning that the Klingons wouldn't experiment with genetic research. Therefore everything is fine then? No.
Because the Augment virus ravaged the Klingon population prior to the U.S.S Kelvin's fateful encounter with Nero, then the Klingons (or the majority of them) should still have disease-ravaged heads in Into Darkness.
So how/why exactly do the Klingons in Into Darkness have cranial ridges?