You know what, Gunslinger Girl (first series). It got the tone right. On one hand you've got cute girls you feel should be protected, on the other hand there is a creepy slow realisation that they are all seriously fucked up due to their conditioning, to the point they don't really have a sense of morality beyond their orders and obsess over seemingly minor things like Henrietta measuring how well she thinks she's doing based on how many bodies she's created for her master.
Despite the concept sounding rather silly (Cyborg Adolescent Girl Assassins working for the Italian Government) it's surprisingly serious in tone, no fan real service and makes a point of being fairly realistic within reason.
Avoid the second series like the plague, read the manga instead. Boring Italian politics aside the later stuff is pretty good at times and further shows how even the stable looking ones have their own obsessions.