Yeah, but if $dst can be changed by a user,

File::Copy($src, $dst);
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can wipe any file you care about. Note that prevention of executing arbitrary commands is trivial using system:

system '/bin/cp', $src, $dst;
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Not any more dangerous than File::Copy.

As example $dst='text.txt; cat /etc/passwd | mail ...'. If this script will be using with root privilege...

Yawn. If the script is executed with root privileges, and $dst = '/etc/passwd', File::Copy("blah", $dst); isn't exactly harmless.

Oh, and if you're going to accept data from others, you ought to be using taint mode anyway. And properly detaint your input.