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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