From How can I use Perl's i option from within a program? the -i option changes $^I which in turn changes how <> works. That means the magic only works inside a while loop that uses <>. Your code with -i added on for me made a .bak copy but cleared the original and printed to the command line. The following code does what you requested.

#!/perl -i.bak

while(<>) {
    print;
    if(eof) {
        print "\n";
        print "##Copyright (C) 2012 by firstName lastName\n" ;
    }
}
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