There is, or was, a fuel pump at St. Mary's, the biggest hbr in Scillies, when we were there in 1999. From memory the fuel comes across as a container on the ferry. St. Mary's was v. busy with all of visitor buoys taken up. The anchoring on the outside of the buoys is dodgy with loads of kelp on the bottom. We just popped in from the less populated areas picked up the fuel and scooted.
Diesel is available at the quay in St Mary's harbour usually in the morning before the Scillonian arrives at midday, give the harbourmaster a call on VHF and he will advise as there is usually a queue but not always. Alternatively you can get red diesel in cans 9-5 from the petrol station/laundrette at Porthcressa or on the quay behind the hotel. All the fuel is provided by Sibley's at the moment they have the monopoly on that one over here. Price per litre when I last bought some was 53p.
When I was last there, the harbourmaster at St Mary's would ask you if you needed fuel or water when he collected his dues in the morning. If you did he'd book you a slot to go alongside and fill up.
There's an article about a West Country/Scillies cruise in a displacement mobo in this month's Motor Boats Monthly, which makes interesting reading.
From the article, I particularly note the following:
"Fuel and water are very expensive in Scilly, so fill your tanks before you leave the Mainland"
Might be worth buying a copy, if you can bear the public shame of being seen with a Mobo magazine in your hands. Alternatively, the Waterloo WH Smith Public Lending Library had a few dog-eared copies left as of yesterday, for reading on the spot....