What we did in our old guild was guild repairs were turned OFF ALWAYS. The only time repairs were turned on was for people of raider level or higher (meaning the people actually raiding) and only at the end of the raid. So basically repairs were only used to repair damaged gear from the actual raid. Outside of that you were on your own. The guild repairs of a raid guild should be for raiders to repair from raids. If you just wonder around and die 10 times doing your dailies YOU should be responsible for paying.
My current guild doesn't do this but I do it myself by only using guild repairs during raids. Otherwise I pay for it myself. It sucks dropping 100g of my own money because I was stupid during my farming but that's my fault not the guilds.