it's doesn't take a lot of CM's to run
...the Cast Member to guest ratio on JC is pretty high. You also have to consider that skippers are not your average just-off-the-street Cast Members.
If this was to ever happen, I am willing to bet it would be because of the cost of staffing the Cruise compared to the number of guests Cruised.
Just because something has lines doesn't mean it's cost effective. JC depends on having a good number of excellent skippers each "servicing" a limited number of boat passengers at a time. This is precisely the kind of money-saving project that Disney has affinity for: no one's going to stop coming if JC goes down, it sells no plush, and it's costly in terms of staff-to-guest ratio.
I just can't believe WDW would do this under any circumstance.
This is where we come back to seeing/not seeing a trend. I think it would be easy to make a business case that JC is one of the less cost-effective ways to keep guests occupied for X units of time, and that the trend has been to maximize this type of cost-effectiveness. I would not be surprised at all if this happened, it fits the trend of valuing bookkeeping entries over guest experience and Disney tradition.
It's always interesting to plot the points where different people realize "oh, crap, that _was_ a slippery slope, after all."
Jeff
PS: Would it be too provocative for me suggest that, had the announcement been "JC definitely closing" directly from Disney themselves, it would have been the 'Scoop who would have pointed out the staffing costs, with excusatory intent?
