I had the same problem, but eventually found a case which works for me. It is meant for a WiiU controller so is the correct length, but a little wider than required. However, I use this extra width to stores my USB cable etc.
The outside of the case is thick foam, so I can happily put this in my briefcase and not have to worry about damage. If it gets squeezed the pressure is spread across the whole case so would likely crack the screen before damaging the sticks.
I suppose it really depends upon your preference. I find my 3DS flat analogue stick a bit annoying now that I'm used to the 7800.