Is the seat-belt sign activation when a pilot goes to the lavatory standard procedure?
In the US they do very similar theater when a pilot needs to relieve himself. There is an announcement that nobody is allowed to come forward, and grim looking flight attendants are blocking the aisles with coffee trolleys. The details surely depend on the airline.

Each of these procedures goes back to some bad incident. The cockpit doors are locked since 9/11. Since Germanwings 9525 (PIC on toilet, co-pilot had a death wish, cockpit door locked), a flight attendant has to replace the pilot in the cockpit. I'm not sure if there was an incident calling for body-guarding a pilot outside of the cockpit, but maybe someone can comment.

Even though it is much more likely to get killed by your angry spouse or just falling down the stairs at home, security procedure theater is in fashion, and it is just getting worse and worse. Yes, it is very plausible that the seat-belt sign activation in your flight was standard procedure to ensure that the PIC could pee in peace.



This photo of Thomas Cook Airlines (UK) is courtesy of TripAdvisor

Some similar reports found in the depth of the internet:


boards.ie in August 2013:



  Noticed this last night on a Ryanair flight.
  
  Internal phone call to stewardess was then followed by the fasten seat
  belt sign going on. We were forced to sit down with a by then crying
  baby (who had been just about dozing off being rocked whilst standing
  up) Once we were all sat down cockpit door opens, one of the pilots
  exits and was replaced by an air hostess in the cockpit. He visits the
  loo, comes back out, rings in, door opens, swaps with the air hostess
  and then the lights go back off. Not a hint of turbulence during the
  time period involved. [...]



flyertalk.com in August 2008:



  In the middle of a flight today from LAX-ORD, the seat belt sign was
  turned on and the pilot or co-pilot came out of the cockpit to use the
  bathroom. As soon as the pilot went back into the cockpit, the seat
  belt sign was turned off. It was perfectly smooth throughout this
  portion of the flight, so it was obvious that the seat belt sign was
  turned on just for the pilot to use the facilities. [...]