In all honesty I have less of an issue with Al being killed off than I do with the poor storytelling. It was a clusterfuck basically. If they knew they were going to kill him off they should have put more effort into his story towards the end, rather than have him basically sit at his desk looking mopey for the last half of the season. He was basically irrelevant all season and the show was poorer for it.
I will admit, unlike a lot of people, I am a Ruzek fan. I do get why people don't like him and have no issue with other people's opinions. I get what they were trying to do with him lashing out at Antonio and going along with Voight but with the shit narrative and the lack of continuity of the way these characters are written it was just off.
Al was his mentor, his first partner and they obviously had a close father/son relationship, hell Al moved in with him so instead of reminding us of that over the course of the last few episodes building up to this, it's just bang in your face. I get his grief and anger, I just wish they'd put some kind of effort into showing the reasons for it. If I recall the last time we saw them interact was when Al drove Ruzek to meet Voight. (I assume that also played into Ruzek's reaction his guilt over not being able to stop Woods, or should have but I doubt the writers even remember that Ruzek was caught up in the Festival of Woods. He knows he let Al down and that would eat away at him, again I don't think the writers are that smart though.). So I get his reaction, I still didn't like it but I got it. (Funnily enough the thing that annoyed me the most was throwing the orange peel on the floor...huh)
No one has a blank sheet when it comes to crossing the line, they have all done it to vary degrees when it suits them. Hell even Atwater has his moments, he beat the crap out of the guy in jail and showed no sign of stopping until he was dragged off him, he taunted a man to pick up a gun so he could shoot him, sure some go way beyond that but they all do it. None are beyond reproach.
I assume (again you can't trust the writers) that for all Antonio's moral grandstanding (I didn't disagree with it) he appears to have backed up Voight's version of events to the IA board because Voight walked out of there to continue on his merry way. So what was the point of his stance if he let Voight get away with it again?
The whole storyline felt like it was cobbled together from episode to episode with no thought to how it would look to veiwers. I remember one poster, a while ago saying the problem with this show is that they try and TELL us how characters feel rather than SHOW it. This is never more true than right now.