v2 is supposed to support user authentication. There are no plans to support that in v1.

Personally I hope they go with OAuth or something similarly recognized.

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For now, you'll need to do your own user verification:

1. User enters his ID,
2. You provide a key for the user to add to their profile on SO.
3. User confirms profile has been modified.
4. You verify key and save ID.

Or something similar.