I'm not sure of the specific wording of the statute, but I doubt very much that it would preclude a repositioning cruise. Other lines offer these trans-canal cruises every year when they move their ships to Alaska for the summer, and then again on the way back to the Caribbean. I've never taken one of these, but I think that some lines actually disembark their passengers in Ensenada, Mexico, and then bus them to San Diego, in order to comply with the Act.
I did a quick search to see what other lines do with repositioning cruises. It looks like RCCL uses San Juan as a destination port when cruising east through the canal. They also have a cruise which departs Ft. Lauderdale and arrives in San Diego (which may mean Ensenada, but I'm not sure about that) and vice-versa. HAL offers FLL to SD, as well as to San Francisco, and a Tampa to Seattle cruise.