Welcome to FT, st.b - sorry to hear of the issues that forced you to seek assistance through these pages and hopefully you'll stick around regardless.
Is London to Rome and back your full itinerary? If so, I wouldn't worry too much about your last name appearing twice, even though the airline is correct in saying that your first port of call in terms of any changes to the booking should be the on-line travel agent. Again, though, you shouldn't have any issues and, in case you have a Facebook account, you could always get in touch with one of the [Alitalia] customer service representatives who will probably add a note to the booking or advise further, I can assure you that they are much more helpful and capable compared to their call centre or back office colleagues.
G