That's what you think, yes. But might I add that The Bible also specifically says thou shalt not kill, yet the crusades were deemed theologically just in the Middle Ages? It's not that simple.
I really can't speak for my Christian brothers, however I think you have touched a very important difference between the two religions when it comes to organization and legislation.
Let me try my best to explain this to you my dear Seven. When it comes to Islamic legislation, Quran is not the only source for it. True, it is the most important and the most definitive. There are 3 more sources:
Hadeeth: Which is the collection of all the prophet's saying. I discussed this thoroughly with Erik before, however I will briefly explain it to you.
Hadeeth has arrived to us by narration. Meaning that for the first couple centuries it was not written down, but narrated down from the prophet up to writing them down (not sure when perhaps 300 years or so.) Anyways as you can see the danger in this technique, thats why guidelines were devised to preserve the authenticity of such sayings. The system has two parts, the hadith itself called "matn", and the lineage of narrators called "sanad". Its a very intricate system, the narrators are/were profiled on different criteria, such is he a good memorizier, is he a liar/ or ever lied, political agenda, did he ever meet the person he is narrating from...etc. Then comes the "matn", is it in accordance with Quran, and other Hadith or not. A hadith could arrive to us from one lineage or 10's of lineages, the more lineage the more trusted. All these factors mix in to create a very well devised rating system, I higher rated Hadeeth would negate a lower one if they conflict and so on.
For more info:
http://en.wikipedia.org/wiki/Isnad (the ratings are on the right.)
Qiyas: or literally measurement, i.e smoking was not explicitly forbidden, it wasn't even available back then. However scholars "measured" this with forbiding one killing himself or harming himself. Same can be said for weed, where it is forbidden and measured with "alcohol" in that it conceals ones mind...and so on.
Ijma'a: Islamic scholars agreeing unanimously on something is the also a source of legislation. One of the unanimously agreed on concepts is the 5 "hurumat". Or that its forbidden to trespressing on another person's (or yours), religion, life, money or any property, mind, "ird" which loosely translates to family but not quite

.
Anyways my point is that, whilst in Christianity all the power is put in the hands of someone in the Vatican (or at least to my understanding), it is not the case in Islam, nobody yields the power. When someone is wrong multiple other scholars, groups, factions...etc will disagree and make it heard. The terrorist bandits, were very much opposed even before 911, and the general consent of Muslim's that this group has gone astray.
I hope you find this insightful, and sorry if talked to much. L)