If I read the agreement correctly, the ban on sending apps with beta version 3.2 applies only to the SDK, not to the tools. If you install the SDK for the application database in the SDK earlier than 3.2 (which probably already exists anyway), you can build using the SDK 3.1 and earlier by selecting them from the Browse menu in Xcode.
I introduced updates to my iPhone apps built with SDK 3.0 using 3.2 beta tools and they were accepted without any problems. Until you build a new SDK, you should be fine.
EDIT: I don't work for Apple, I'm not a lawyer, blah blah. But it worked for me, and the warning only says βiPhone SDK 3.2β. Xcode tools are not mentioned.
Arclite
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