Why Can Pilots Still Shut Off Transponders?

All systems on board an aircraft can be shut off for a number of reasons. In case of a power failure, the pilot must choose what functions are the most essential to the continued operation of the aircraft on the limited battery power remaining. A transponder may then become nonessential. Similarly, if it is faulty and is the cause of an electrical fire, power to the transponder must be able to be shut off.

I can't read the article as it is behind a paywall. However as a pilot I can tell you that you are generally meant to turn off your transponder while taxiing on the ground. Also you shouldn't turn it on until you actually have a transponder code, as you'll be transmitting an invalid code (possibly conflicting with another flight).

Perhaps airliners should be made so that you can't turn off the transponder while in the air.

Also, we don't know if they did actually turn off the transponder or not.

The normal transponder system is not designed to be on all the time. In light aircraft it's just a box on the dashboard like http://www.ebay.co.uk/itm/AIRCRAFT-B727-ATC-TRANSPONDER-P-N-...

that you can turn on if you are flying into controlled airspace.

What I think they should have is a new system that pings the location and other data to satellites that can't be turned off and will work anywhere unlike radar transponders.

One simple situation in which you would like to switch modes on the transponder (ok, so this is not technically shutting the transponder down) is when - for example - a loss of cabin pressure occurs. Since most (all?) commercial arliners will have to perform an emergency decent to somewhere around 10,000 feet it is dangerous for transponders to operate in TA/RA (Traffic Advisory/Resolution Advisory) mode and give climb or descend instructions to avoid other traffic. In this case pilots switch to a "squawk only" setting.