Several likeable characters have died. Sophia and Dale come to mind. While it was easy to see that Shane would lose it and be killed off the other two weren't as foreseeable.
I think Dale and T-Dog's deaths were telegraphed. Both reached some sort of moment where their opinions/moral view was not accepted; Dale regarding the captive, and T-Dog's desire to give the inmates a chance. Predictable scripting usually has characters rejected because of their moral convictions rewarded with death so the characters' mortality was written all over the walls.
Same with Lori: in modern zombie productions, the trens seem to be that preganant characters have one kind of complication or another: in the Dawn of the Dead remake, "Luda" was bitten, dies and gave birth to a zombie child. Once Lori found herself knocked up, you just knew it was not going anywhere good either for her or the child, so Lori's death (in a world with no medical support) was easy to see coming.
Also in this season they've made one of the most likeable characters on the series - Andrea - much less so as she's seemingly switched sides for safety's sake. I didn't see that coming either.
Wait a second--she's one of the most likeable? She's been a major ass throughout the series. In season one, she's crappy to Dale. Season two she's running around trying to assert herself as a gunslinger, screws a psychopath (Shane), remains crappy to Dale, and worst of all, she plays some irresponsible game with a teenage girl (Beth) when the latter was considering suicide. Jump to season three, and with half of it in the can, she's still an ass with her lust for the Governor, ignoring Michonne's concerns, etc.