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 (the team has said).
For now, you'll need to do your own user verification:
- User enters his ID,
- You provide a key for the user to add to their profile on SO.
- User confirms profile has been modified.
- You verify key and save ID.
Or something similar.