How to install developer certificate/private key and provisioning profile for iOS development via command line?

The always allow GUI is being triggered because codesign hasn't been given an acl to access your private key. try this:

security unlock-keychain -p <my keychain password>
security import Certificate.p12 -k ~/Library/Keychains/login.keychain -P password -T /usr/bin/codesign

The -T flag tells security to allow codesign to have access to the keys you are importing in Certificate.p12.

I found hints from: http://lists.apple.com/archives/apple-cdsa/2010/Mar/msg00021.html

The command is security. I'm reading manual page. I'll update this answer later after trial :)

--(edit)--

First, we have to give 'Always Allow' access to the certificates/keys in the Keychain manually once. I don't know how to do this without GUI.

And run the command security unlock-keychain before running build tool for every session. I've used SSH, so I had to execute it once for every login sessions.