I wouldn't say light side/ dark side thing. It was more if you consistently played Shep one way rather then bounce between the two approaches..
Seriously, it wasn't that hard to have everyone survive. You did the loyalty missions, you picked up the ship upgrades. And you made a couple of common sense choices in regards to a> who can hack/deal with tech - ie: Tali, Legion or Kasumi, b> which characters have experience in leading teams (Garrus or Miranda pretty much, possibly Jacob), and c>who actually has serious biotic powers (either Samara or Jack)..
I have no problem with a reputation system working in this manner, reflected in NPC dialouge responses. But, not having enough points should not prevent you from taking specific actions, and those unavailable options shouldn't be dangled right in front of you for no other reason than to piss you off either.