Just to clarify, is there anything in this that affects the direct exchange of bitcoins for goods and services?
No. FinCEN seems to be focusing on the exchange of virtual currency (bitcoin) for "real money". The direct exchange of bitcoin for goods and/or services was specifically excluded from FinCEN registration requirements.
Great! So a purely Bitcoin sub-economy is still OK. Although, presumably if your earnings are purely in Bitcoin, you'd have to exchange some of them into USD to pay income tax.