I get the argument, however, there are two reasons why the rule is beneficial IMO:
1) The cockpit door will still be open whenever a pilot wants a break (and returns). How does another person entering when one exits be a greater safety risk?
2) There is the psychological factor: Solitude is a major factor in mental issues including suicide. Most people will feel more at ease around other people and interacting with them, or at least feel compelled to not act improperly.
When you’re alone, it’s not only you perceiving and being affected by your actions. For reasons ranging from our inherent sense of shame, not wanting to be seen or detected, to not wanting to hurt others, we don’t do things we would do on our own with another person around. Think of yourself: How many things aren’t there that you’d do when alone, but definitely not around other people, let alone a colleague? And the shame when you mistakenly realise you’re not alone - like your mother entering the room while you’re masturbating.
And a locked aircraft door is definitely a barrier between a lone pilot wearing noice-canceling headphones and the other people onboard, enough to create a sense of solitude. A suicidal pilot would without a doubt be far more likely to crash aircraft when alone than with another person on the flight deck he could talk with.
Let’s just look at statistics: ALL pilot suicide crashes (Germanwings. Silkair, Egyptair, LAM Mozambique and probably MH370) involve the same scenario: One pilot alone on the flight deck. If having two people on the flight deck isn’t a deterrance, why did these pilots wait until the other pilot left the flight deck before committing the act?
The only instance of pilot suicide with another person on the flight deck, was a Royal Air Maroc flight in 1994, where the captain was reported to have had romantic problems, also involving the female first officer rejecting his advances (e.g. a motive to hurt the person sitting in the flight deck!)
Apart from their presence alone being a deterrent, the other person could convince the suicidal pilot to retreat if he/she inexplicably would try to crash the plane («Please, don’t do it! Talk to me instead, I want to help you! Think about the passengers and their families!»), or let the captain inside.