Climate change is going to have a serious impact on many foods, guacamole being only one of them. As temperatures rise and storms increase in intensity, the growing conditions for many foods will suffer. Joining guacamole will be coffee, chocolate, French wines, bananas, and many more foods that will become scarce, expensive, or just plain gone.
When a public company has a poor result they will always blame it on outside factors out of their control, so Chipotle smartly is shifting the blame away from bad execution on the companies part and pinning it on a controversial topic such as global warming, it's a smart move from the company, overall I think the actual answer is probably a combination of overuse and global warming.
The supposed guacamole crisis is not due to overuse by restaurants like Chipotle, but rather is more likely occurring due to global warming effects that are being experienced in the areas in which avocados are grown. A longer or shorter growing season, in addition to drought or too much precipitation can all have severe consequences for crops.
How could global warming possibly be the cause of a guacamole crisis. I think Chipolte is probably having a crisis with guacamole because it may be getting too expensive for them to keep offering to customers. Some customers don't finish the guacamole and in turn, it ends up being thrown away which ends up costing the restaurant more money.