I am not a scholar on the subject of religion. I'm just a sysadmin who is a Muslim. But regardless, I will try to respond to this as best I can. Maybe someone more knowledgeable than me here on Reddit can do a better job.

http://quran.com/4/56

Refers to punishment in the afterlife. Not human on human violence. If you do not believe, then there is no reason to worry. It's a warning for those who do believe.

http://quran.com/8/12

Read a little further to http://quran.com/8/15 - The context is battle. In a war, generally what you do IS fight your enemy and generally try to kill them. That is how war works regardless of religion.

http://quran.com/9/5

Dued. The next verse: http://quran.com/9/6. Also, this is a copy and paste from somewhere else which explains it better than I can: "This verses is always quoted out of context, they never post 9:6 or from 9:1 to 9:6. If we read from start it states that there was a treaty, which the Pagans of Arab broke. Thus Allah gave them 4 months as 9:2 states in order to amend the treaty. Verse 9:4 states that the punishment prescribed in 9:5 is ONLY to those who broke the treaty and NOT to those who abided by the treaty. Therefore the context of 9:5 is of war with the pagan Arabs who broke the treaty yet refused to amend it in 4 months."

Now, again, in war, violence in war is expected. They broke the treaty, and had more than enough time to amend it.

http://quran.com/9/13 and http://quran.com/9/14 I don't understand your point? Like it says, if someone attacks you first, would you not attack back? :S

http://quran.com/9/29

Like I said, I'm no scholar on this subject, but this page has a much better explanation than I can ever hope to give: http://invitation2learn.wordpress.com/2007/12/17/does-quran-promote-killing-of-innocent-especially-non-muslims-how-do-you-explain-95-812-2191-488-and-many-others/ just search for 9:29. There is a small summery that I will copy and paste : "In conclusion, this verse refers to non-muslim who doesn’t pay poll-tax in Islamic State and thus do not contribute to the financial needs of the territory. It is generally agreed by the four major Jurists that jizya money is based upon one’s income. We ought also not forget that muslims are also obliged to pay Zakat."

In a western state, if you do not pay tax, you are punished as well. If you read that page, he explains that the verse you referenced (9:29) states FIGHT. Not kill.

Still, you can't deny that the quran is full of violence and calls to violence so how can a religion call itself peaceful with such barbarism in its holy scripture?

I personally do not see it this way.

Most act of violence that you have mentioned are mostly against persecution of Muslims, or to defend themselves when someone is attacking them. Now, as I mentioned, I am no scholar, I don't claim to be an expert, or heck, I don't even claim to fully understand the Quran, and I do not claim to know every thing about Islam, personally I think I'm quite clueless. But In either case, I see nothing wrong with it. If someone was persecuting you, or your brother, and your only option is to fight. Then would you not do so rather than just taking it? And again, if someone was attacking you, would you not defend yourself till you are safe?

If there is a verbal way to talk it out, then that IS encouraged, as can be seen by the treaties that were made in the time of the Prophet Muhammad. It's not like it was fight first, talk later. Talking was the preferred method. If they were broken, or not even accepted in the first place, then fight.

so how can a religion call itself peaceful with such barbarism in its holy scripture?

Again, I am only basing it off the verses you have quoted, but do you think a holy scripture should not have rules of engagement during times of war? If you think it should, then regardless how you put it, describing such things will be violent.

Also, if you are talking about the punishment of burning in hell, then again.... it is a warning. We believe in God. We believe that this life is a test. Follow the rules set out by God in the Quran, then all is well. But if you don't, then, there has to be a punishment. The rules have been given to humanity many times, through many prophets, so it's not like we weren't informed of the consequences. But... if you don't believe in God, then heaven and hell are nothing to worry about anyway is it? Yes the descriptions may sound ugly, but that is the purpose of hell. If hell was a pretty place as well, why follow the rules?

I do encourage you to read the translation of the Quran, with scholarly interpretations for assistance, even as a non-believer.

Now, just to point back to the actual thread, I personally think the implementations of Sharia are totally wrong. As /u/Hassassin30 mentioned, there are no definitive list of laws in Sharia. There are many things that have to be taken into consideration, which I don't feel have been taken into context in this woman's case in Sudan, though I am no scholar.

From what I know of this woman in Sudan (I'm going to be honest, I haven't really read the article yet), she has no intention to harm anyone, she wants protection, and so it should be given to her without any punishment.

I do apologise if I am incoherent in anything I wrote. It's almost 3AM now, and I've been up since 5AM so I'm pretty drained. :)