Have you considered using expect? Here is a sample expect script that will spawn the CPAN shell, answer "no" if appropriate during the configuration prompt, and quit when it sees the normal cpan> prompt. If the manual config prompt doesn't appear, the script will still catch it. This was written in the previous few minutes, so it can really be cleaned up and set to do something other than smartass remarks when something goes wrong; however it seems to do the job:

# 10 second time limit for one of our conditions to be met
set timeout 10

eval spawn "/usr/bin/perl" "-MCPAN -e shell"

expect {
    "Are you ready for manual configuration?" {
        send "no\r"
    }
    "cpan>" {
        send "quit\r"
        expect eof
        exit
    }
    timeout {
        puts "\nWe ran out of time\n"
        exit
    }
    eof {
        puts "\nOh noes, unexpected EOF\n"
        exit
    }
}

# This will only be reached if a default configuration keypress was re
+quired
expect "cpan>"
send "quit\r"
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