Motorised faders work out about £20 each which would amount to £1000 for 50 without the extra hardware and development cost. That is pretty steep!
An alternative might be to use push / pull solenoids like these from eBay at £2.50 each plus micro-switches and drawbars. 50 of these would cost £125 plus associated electronics and development. The drawbar could be designed with sufficient friction to hold in place but free enough to allow solenoid to move. Micro-switch would detect position. Microcontroller would provide USB or network interface to host.
[Edit] I know they may not be called drawbars on a church organ but it was the work that came to mind as I typed this!