Pardalis, I have spent some time in the Middle East. Muslims are just as stupid, bigoted, and ignorant, if not more so than the rest of us in some cases (I would argue the lack of a good secular education system is whats holding many people back though, so it is not that they are "inferior" as much as they are attempting to make the world fit a religious-arab nationalist-anti-semitic world view that they have been spoon fed since birth). I have several perfectly rational Muslim friends from growing up however (mostly folks from Indonesia) and it pains me to see someone drag the faiths of my friends along for a ride into stupidity.
Back to the Tomahawk. No. Just no. From my limited exposure to military hardware or computing, generally the electronics packages are little "black boxes" or a purpose built component for that particular platform. Just as an example, you cannot drop the optics/range finder package for a Bradly fighting vehicle, into an Abrams tank, despite the fact they are doing the same basic function. These parts were not designed for plug and play, or easy compatibility.
The Tomahawk was designed to fly nap of the earth, as fast as its little engine could go, to a series of waypoints before going either terminal (with either a conventional, or nuclear payload), or dumping out a series of submunitions. It was not designed to fly evasively. It was built around a simple, fast, brutal flight plan with no deviation. Which is really all a missile needs actually.
The Tomahawk does not even have the programming to understand half the flight surfaces on a Boeing 767, let alone use them. Its a poor choice for a guidance package, and I can only imagine how many weeks, if it were possible at all, it would take to get a Tomahawk guidance package to even sort of fly a plane, and even then it would require hundreds of people working on the plane-software-hardware integration.
All of whom might raise eyebrows at just why they are building a commercial jetliner for the expressed purpose of flying it into a building.
If you were going to build a guidance package for a jetliner, the easiest, and least complicated way would be to build a custom job, as it allow you to build something that fit the plane, rather than mangling a Tomahawk's guidance package, and futzing with the plane to make them both work together. What you are proposing is a stupid complicated solution to a problem that would be better approached in a different way.