@Quarian Master Race. You hit upon a point i've been struggling to make (and gave me a laugh along the way) I actually liked the geth mind you, I'm a certified hippy toaster hugger that way! 
But some of the renegade actions just made so little sense. There should be repercussions for such flagrantly abusive actions. As it stand shep can be a complete jerk and the ME univerese just shrugs it's shoulders. When theres no comeback, it lacks meaning and just becomes redundant.
@snakecode
I get what your saying about the having a scale to tell us how good/bad we are being, not really being mature, but in truth I don't mean to suggest that we have an actual bar, representing our, for us, the players to look at, level of goodlyness or badishness (totally not words but i'm using em anyway) , but if your going to have nuanced dynamic reactions from other npc's and the game world at large that information needs to be tracked internally atleast within the game, or you just can't build that kinda of depth into interactions. What I'm trying to get at is how developers define actions internally so as to build believeable and complex reactions from NPCs as a consequence to our actions, thereby giving those choices weight and significance. At the moment the thinking behind say, the hen'garel example, which I call simplistic and poorly thought out and then executed makes for a character that behaves in an irrational or unbelievable manner, to then follow that up with no consequence, no fall out with other characters. It just comes across as hammy.
As others have been saying, alot of these situations, in game, might be subjective, but for the sake of narrative the developers need to establish some form of internal system by which weight is given to actions in a for/against format, or good/bad. With clearly defined consequences for, us, the players to discover. Having the player smack Al Jhilani in the kisser was a hoot first time around. But once the laugh wears off and you play the game again and take the same choice, suddenly it's just stupid in the context of the game and the PC's current situation.
Fortunately developers should be aware of the a games story and content, which would allow them to program a system that, if done well and with considerable for-thought, could be very deep, very nuanced and very complex. We, as players would then have the joy that is "peeling back the layers of the onion" and discovering the nature of the choices we make through the consequnces and impact of our choices.
The withcer series started to do this, my PC would make a choice that, on the face of it, seemed like the right descision for his personality, help people, only to have the situation shift and suddenly that peasant I helped turned out to be an ass that goes on to kill somebody else. Unfortunately the witcher stop it right there. The developers didn't expand on the idea, there are no companions that react and play off of the decisions I made and the bleak crapsack world, remained a bleak crapsack world regardless of the action of my character so I didn't really care too much.