I had a similar situation unwittingly on my race bike. I thought it would be a good idea to drop down to a 13 - 29 rear cassette to go with my 53-40-30 triple, so that I would be able to get up pretty much anything. The investment paid off - it was probably the only reason I got up Bwich-y-Groes after 300km on the Cambrian 4C, and that gruesome top 2km of the Col du Glandon. My race bike has been stripped down to steel, repainted and rebuilt by Argos Racing Cycles, who pointed out that Mr Campag recommended a long cage and the current set-up was at risk of sending the rear-mech into the wheel and the slight clicking in the granny gear was that sound of impending doom.
It didn't happen in the 6 years I rode with this set-up (and I never heard the clicking when I dropped down to that 28" ratio as I was more worried about maintaining snails paces up tarmac-defying inclines) but I have secured a long cage rear mech at astronomic cost through the wonders of eBay as even at the price I paid it is cheaper than a new rear wheel.