I had a horrible time getting information on this in 2008. It seems to be similar to our emissions testing here in Washington state in that you have to have the car to get the sticker. I don't have a clear cut answer, but what I have learned is this:
Any car rented in Germany will have every sticker you need for driving anywhere in Germany. (since I rented in Munich, my problem was solved)
Some people have been able to contact their car rental agency in other countries and let them know they need the sticker. They were told it would be on the car (not sure how that all turned out, since they were posting before the trip, not after)
Worst case scenario: You pick up the car and you don't have a sticker. Take some information on where you can stay outside the zone in Munich. Cancel previous reservation and re-book. Use public transportation to get into downtown Munich.
or
No sticker: see if you can store the car at a rental location outside Munich and use public transportation into the city. (i.e. you rent from Hertz, see if you can store the car at the Hertz airport location for a couple of days and ride the S bahn into the city.)
Yea, I don't particularly like those options either, but hopefully your rental car will have the sticker. They are good for the life of the car, and since many drivers use cars in multiple countries, we can optimistically hope that rental agencies will get them for you. (But always, always have a back up plan!!)