Hi Tugay,
2003 native mode should be alright. I would only be worried with ADFS running on 2003 native mode, but this seems to be alright as well:
Most AD FS 2.0 features do not require AD DS functional-level modifications to operate successfully. However, Windows Server 2008 domain functional level or higher is required for client certificate authentication to operate successfully if the
certificate is explicitly mapped to a user's account in AD DS.
http://technet.microsoft.com/en-us/library/ff678034%28v=ws.10%29.aspx
hope it helps
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