You are not being taxed again. Until it is reported on the return it has not been taxed yet.
When you had money taken out of $4,500 you get credit for that on your income taxes. The tax is determined on the Pension, just like others getting a W-2 and having taxes taken out of each paycheck.
So the return then determines the correct tax based on all the income and the deductions and this will determine if you paid in too much or too little when you took the money out.