I don't understand how high avocado prices could cause Chipotle to loose money. Guacamole is an optional add on why wouldn't they just raise the price of the guacamole to reflect the market price of avocado or use avocado futures to hedge their price risk.
Not saying they don't do stuff like that all the time, there's just more of a lag between a commodity price rising and a chains ability to raise the price of the end product.
These kinds of decisions are made over fairly long time frames. Someone will be studying the likely effect of each possible price, others are forecasting how long avocado prices might stay high. Lots of disagreements, oh Jim thinks it will stay this high for a year, Mary says another month. Those things have to get worked out before even the decision will be made.
It just takes time and it would have to hurt first (sounds like that day is here), but they will eventually raise the price.