Ben,
Running the cfg tool requires that you have rights to log on to all mailboxes. There are several methods for granting those permissions, one of which is the vbscript. Another method is to simply grant Receive As at the Mailbox Store level for the account you want to run the tool as. Receive As = Full Mailbox Access. If the account you are using has an inherited Deny for Recive As, then you can edit the Deny and place an explicit Allow. Explicit permissions will override inherited.
If indeed Send As is required (which I'm not sure it actually is), then you can grant that easily at the domain level. In ADUC, make sure you have the advanced view shown, then go to the security tab on your domain properties. Go to the Advanced permissions, then add the account, and under the "Apply Onto" section, select "User Objects". You will then see the Send As permission listed. In my testing, however, I have not required Send As rights in order to run the tool in update mode.