I personally think the roses in the empty chairs is a beautiful idea, however you stated that your family is having a hard time with this loss. If that is the case, you might not want to have the rose sitting in an empty chair next to your mother during the service. This might be more than she can handle. Check with her before you plan this.
For my parents I did a memorial candle and a picture of them on a table in front of the first pew of the church. My son lit the candle after he walked me down the aisle. My husband and I placed a single red rose on the table as we exited the ceremony. (This proved to be a tear jerker to many of our guests)
Best of luck!