That is the most stupid explanation for an electrical problem I've heard in a long time, sounds more like they are complete morons looking for an excuse for their own stupidty. If intake noise and vibration caused electrical failures my car would be completely dead by now, I've been running my scoop driven ram air intake for over 45,000 miles on my 2000 RS, it's likely louder and more vibration prone than any other intake system out there yet all my electrical systems are still operating, including my factory alarm.
If gravel roads, rally-x, and repeated airborn excursions haven't caused electrical problems for me or the Subies I've worked on or played with, I doubt your intake was the source of the problem.
I would suggest finding more intelligent service people, and as others have said, make them prove it caused the problem.
Hope you get it fixed without any more hassles