See clip from Attorney Rajiv S. Khanna's conference call video that addresses this question.
Answer is yes. They can't convert within the United States, but they can go outside of USA and try to get F-1 stamped and come back. That does not get rid of two year residency visa. However, remember two year residency visa requirement only says this: if you have J-1 or a J-2 which is subject to the 212 (e) HRR, you cannot convert to H, L or Green Card, but you can if you want to change to F-1 visa but not within the United States as far as I remember. It does not allow the change of status also. So you can always get a visa stamping done and you can do it without the waiver, F-1 does not require waiver. However if down the line you decide to convert to H-1, your J-1 holding spouse either must have received the waiver or a home residency a fulfillment of 2 year residence abroad to the home country.