As advancement, they are unaligned but it is not clearly written.
In Black Crusade - Core Rulebook, Chapter 6: Psychic Power, page 212:
Certain powers, Nurgle, Slaanesh, and Tzeentch Powers, are
Aligned with that god. This has several effects.
First, taking one of these powers counts as an Advancement
that furthers a Heretic’s alignment with that God. Someone
Aligned to Nurgle taking Nurgle’s Rot increases his Alignment to
Nurgle by 1.
So we see that only the power aligned with a paticular god increase the Alignment.
And the schools of telepathy, telekinesis and divination are special in way that they are not only used by Chaos agent, but also by Imperial agent. For this I can refer you to the other books from the WH40KRPG.