Post 9/11, it is more common to wait for pilots to wait for the other pilot to use the restroom, then lock the anti-hijacking door. At that point, there’s effectively unlimited time to down / hijack the plane.
If you sit up front its not unusual to see them go through this dance which involves barricading the front galley area with drink carts first.
I remember one time on Delta sitting upfront in first and needing to use the bathroom immediately after waking up from a short snooze.
A flight attendant was standing in front of the galley and started barking at me that I needed to sit down when I started to get up. Baffled by this, I checked the seatbelt light, which was off, and tried to explain that I needed to go the restroom, only for her to repeat that I needed to sit down.
Only afterward, after I saw the pilot sneek out of the bathroom, did I put two and two together.
I understand the need to be vigilant, as well as the fact that you don't want to indicate an opportunity for malice by telling passengers that the pilot is outside of the cockpit.
So I’m sure there's no easy way of dealing with this. But blocking the way with a cart will have many, myself included, unconsciously waiting for the cart to be out of the way. Whatever the case, I don't think barking orders is the smartest thing to do, as it risks escalating the situation by evoking a response of equal weight.
Of course the pilot should be able to flip the status to “occupied” before they even get up, that way no one gets up as the pilot is making their way out, and it kind of gives them priority (which they should have anyway for obvious reasons).
The stress in this situation was caused by the flight attendant escalating the situation.