OK we can start with these violent passages but I suspect this is going to be futile as you're likely to reply with something saying oh but in the historical context X or this is nulified or doesn't apply because of Y etc... and that is a moderate interpretation, whereas a fundamentalist would interpret things differently.
http://2pm.co/demo/2500/9/5/
Like i said miss parts out and taking things out of context, funny you should choose this versus as is is typical quote used by critics and Terrorists.
Firstly you should read the being of the chapter 9: Surah Taubah, you will see that their was a peace treaty between the Muslims and the Mushriks, the mushriks violated it and were given 4 months to make amends otherwise war could be declared against them.
Now back to your quote:
“But when the forbidden months are past, then fight and slay the Pagans wherever you find them, and seize them, beleaguer them, and lie in wait for them in every stratagem (of war); but if they repent, and establish regular prayers and practice regular charity, then open the way for them: for God is Oft-Forgiving, Most Merciful.” [Al-Qur’an 9:5]
This verse is quoted during a battle to boost the troops moral. e.g. If you find the emery kill them don't be scared.
The next verse says.
"If one amongst the pagans ask thee for asylum, grant it to him, so that he may hear the word of Allah; and then escort him to where he can be secure that is because they are men without knowledge.” [Al-Qur’an 9:6]".
Like i said before you have to read the whole Quarn as their is other verses regarding rules of warfare, I can add them tomorrow and look over the other two quotes off to bed.