Upgrading the BES will not induce the Send As, but installing SP2 on the Exchange tools might do it. It's not an issue you get from RIM, it's purely Microsoft.
While I do agree with upgrading the Exchange portion to SP2, the best way to avoid the Send As is installing any updates/patches that can induce that.
The biggest issue with upgrading the BES from 4.0 to 4.1 is the DB upgrade failing. Just back everything up. You can always get it working.
How many users do you have on the BES? Just backup the DB and perform the upgrade, it usually works but the there are times when it fails.
The "horror" stories can sometimes be traced back to unsupported configurations also. You have a pretty standard setup, I wouldn't worry about it.
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