No. Hainan and JetBlue absolutely have an interline agreement.

The interline agreement is what lets the two airlines sell a trip as a single ticket. If the interline didn't exist then the trip wouldn't be bookable that way. When airlines agree to interline they can choose to do ticketing or baggage or both. JetBlue does both for all its interline partners.

The "problem" in this case is that JetBlue doesn't do departures out of Terminal E where your flight on Hainan will arrive. The bag should be tagged all the way to Orlando when the passengers check in with Hainan in China. The "strange" part is that in the US all bags are claimed at the point of entry for Customs clearance. So the passengers will have bags tagged to Orlando show up at baggage claim in Boston. They must collect the bags there and go through Customs.

Once through Customs the bags get dropped back off into the airline system. The point in question here is whether JetBlue has recheck facilities in Terminal E or not. I would think it does even without departing flights since it has other international arrivals into Terminal E and those passengers might also be connecting onward. I've asked the company to clarify and will hopefully get an answer soon.

But it is absolutely not an issue of interline or not. The two airlines have an interline agreement that covers baggage and ticketing.