Is it just me - or does BG2 put forward rather strange moral standards every now and then?

Spoilers, lots of!

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1. Cernd's single parent problems
During his personal quest Cernd is treated like the scum of the earth by everyone he ever knew. The given reason is that he left his wife to pursue his plan to become a druid. Sure, if responsibility means that he has to give up his chosen purpose in life and to resort to an existence he doesn't want, he's probably guilty... Being unaware that his wife was pregnant, when he left, I simply don't get it why Bioware tries to stylize Cernd as disloyal coward (who faces his final "punishment" in the epilogue after finishing ToB for the way he chose). It's almost absurd to blame him that his ex-wife made out with a psychopathic nobleman who enjoys tea parties with liches. Furthermore, when he finds out about his child, he is without any hesitation willing to take responsibility. In fact, Cernd's behaviour seems more consistent than Keldorn's who likewise favors "career" over family.

2. In corrupt officials we trust!
Ah, Anomen's infamous quest... You are forced to choose between resorting to vendetta and leaving the case to the at least partly corrupt authorities. The latter is presented as the correct solution which is rewarded with a wisdom-boost. Quite the contrary of what you do all the time while playing BG! As an adventurer you are expected to investigate further and more often than not to take the law in your own hands instead of thinking "Well, brave Lieutenant Aegisfield will surely arrest the scallywag behind the skinner murderers!" - and usually the quests don't consist of gathering of evidence only, but also involve execution of the culprits. That's pure self-administered justice. Sure, Anomen as an aspiring knight of the Order of the Radiant Heart may be a special case, but nonetheless self-administered justice is stigmatized as wrong during his quest, while it seems perfectly okay during the rest of the game. Double moral standards in my opinion.

If you kill the paladin in the Graveyard (the one who's mourning for his son) you don't suffer any penalties. Apparently the man should have died for his lack of attention :D

It's hypothesized that Cernd knew that his wife was pregnant. And, really, if you're called to be a druid, you must be at least somewhat aware of that sort of thing, even on a subconscious level.

That's the woman in you speaking, Illumina ;)