GSX cannot possible cause crashes in flight. And yes, even if you say it doesn't happen without GSX, it still doesn't mean GSX is the cause.
A common cause of instability in the sim, is issues with the Navdata, either the Navdata API or the Navdata itself. This was proven by a very minor issue ( a duplicated airport in Navigraph and also in the default Navdata ), which caused a recent World Update to end up in confirmed crash.
GSX clearly need to read the Navdata, otherwise it cannot work. However, you can reduce the chance for this to be happening, if you use the "Disable in Cruise" feature and do the whole flight with the GSX menu disabled on the Toolbar (dark icon) so GSX will never query the Navdata along the flight, reducing the chance a problem with it might mislead you GSX caused a crash, when in fact it was some bad Navadata encountered along the flight.
