Checking into the BVI's and back to the US is pretty easy and pain free. Plus most folks who sail out of the BVI's never get to see the usvi even St. John which has some great snorkeling, anchorages, and hiking. Cruz Bay is a great place to visit, re-provision and shop. From what I have been told you actually save a day by sailing in and out of St. Thomas. Don't know I've never left from anywhere else.
No matter what you do you won't make a mistake visiting the area. It is beautiful and a great place to visit.