What you are addressing in your OP is our (that is, people raised as or majorly brought up in the JW faith) ethics and morality. I think possibly what you're realizing is that you now have to work to reprogram your concepts of these.
We have been taught and brought up to believe them to be completely grounded in our faith and the bible. For example, the fruitages of the spirit (love, joy, peace, long suffering, kindness, goodness, faith, you remember) are called, "... of the spirit."
JW doctrine this teaches that without the spirit these characteristics cannot be possessed adequately - and as a nonbeliever in JW dogma you certainly wouldn't have them.
In short: our religion (and indeed most if not all) teaches there is no morality without religion and so coming out of it leads to this inevitable quandary of 'is there right and wrong?'
I've just finished reading several books by Sam Harris and I highly suggest you read one in particular: The End of Faith. I also suggest reading Undeniable by Bill Nye. What you will see discussed in these books (I believe more so in Undeniable) is the subject of altruism and the development of our morality by evolution. Science has shown that ethics and morality developed this way and is absolutely not reliant upon faith to be had.
Harris provides a very good example by a discussion about collateral damage that shows how morality can be measured. In the recent and current battles in certain middle eastern areas the United States may blow up a building targeting a very evil man or group of men. In doing so, it isn't unheard of for innocents to be killed (and he gives an example of this) possibly even children. The United States views that loss of life as a tragedy and regrets very much the loss of innocents. This is called collateral damage. By comparison, a Muslim may strap a bomb to himself and try to blow up an American official but in doing so kill a dozen children and several adults. Unlike the U.S. response to such unintended loss of life, this is celebrated and praised. Further, the man who blew himself up is celebrated joyfully by his neighbors at home and even his parents are happy.
Thus is the difference between collateral damage and terrorism. It's the intent and he subsequent reaction that measure the morality. Attempting to kill an evil Muslim who is intent on slaughtering as many westerners as possible for no reason other than his faith is the moral and right thing to do to save lives, mourning the loss of innocent life in this effort is the moral and right thing to do because it's tragic. The exact opposite can be said of the other side.
Ethics and morality are absolutely not monopolized by, and in fact do not even originate with, faith and religion. The belief that they are is the only reason why anyone would ever view 9/11 as right, in the case of your one examples. This is a fact of reality and one I suggest further reading on immediately.
