in the BMWs of certain vintage (E53 is part of it) the GM wakes up even when the ignition is not on and the key is out - the design is to prep the car for start of the engine, blah blah blah... Of course, the airbag (SRS) system wakes up when the ignition is on and it goes through the self-check... i would just suggest using a metal coat hanger to secure the plugged airbag in suspended state to avoid any issues... on the other hand, an airbag light can be easily reset using the software and a cable - I was working on non airbag wiring in the passenger seat when i set off the airbag light... no biggy, just reset it with the INPA...
so, this is definetely not the end of the world, you can do this work as you wish, since you already know what to do and what to avoid...
make sure you don't play with the windows too much before you fix it - if the cable cuts into the plastic pulley of the regulator, you will need to replace the regulator, as the pulleys are riveted to the rails...
otherwise - just carry on, it seems that you are fully capable of this repairs...
BTW, do we have pics of your ride???? C'mon, post the pics, show off!!! we always like checking out each others cars....