From what I've read Blackberry Enterprise Server (BES) doesn't require direct access to the Information Store - it accesses Exchange through MAPI. Given this, I am surprised that RIM have programmed BES services to be dependent on the Exchange Information Store.
After MUCH research (a day of reading...) you can change a few BES registry entries. By doing this BES no longer depends on the Exchange Information Store - it just ignores whether it is running or not.
Check out Blackberry KB01274. BlackBerry Search Results