The Allow/Cancel prompts will remain in the final product. The difference is you'll most probably see them less often, since it's still being tweaked. It's a necessary evil. Any operation that requires administrative privileges will bring up the prompt so that the user can temporarily elevate to perform the operation. UNIX-based systems (including Mac OS X) work the same way. It keeps the system more secure since rogue applications can't damage critical areas of the system without user intervention.
The built-in "Administrator" account is exempt from UAC, so if you login using that account, you won't ever see the prompts.