Yes, you should omit it from the Deductions and Credits section.
If you already entered the information about your rental property mortgage interest in the Rental Income and Expenses section, then there should have been a box that you could check stating that any personal portion of that interest would automatically go to the Schedule A without needing to be entered again. While you are going through the Schedule A section of mortgage interest, you should see a message on the screen regarding interest that was already entered in Schedule E. Therefore, you do not need to enter it again.