Actually, I think the example code as it stands is in the spirit if not the word of what the refactoring pattern is meant to avoid. While $arg_ref is a local temp, it's still a reference to the original arguments (a hashref), so updating it would update the arguments pass, which is what this pattern is meant to address. Hence the introduction of the secondary temp. That said, for the sake of completeness, the completely un-refactored code might look like this as you suggest:

sub discount{
    $_[0]->{input_val} -= $_[0]->{input_val} > 50 ? 2 : 0;
    $_[0]->{input_val} -= $_[0]->{quantity} > 100 ? 1 : 0;
    $_[0]->{input_val} -= $_[0]->{year_to_date} > 10000 ? 4 : 0;
    return $_[0]->{input_val};
}
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