I was also really surprised about this after reading the article. I look around to know a bit more about the Airbus design and arrived at this [article](
http://msquair.wordpress.com/2011/09/16/pilots-in-the-loop-a...). The problem is not that they are averaged, but it seems to be that they are not coupled.
It seems that it has been known since 1987 that pilots prefer coupled sticks:
In a 1987 evaluation of side stick controllers Summers et al (1987) found that under simulated ‘surprise’ hand overs pilots Cooper Harper rating of the schemes were (in descending order):
Coupled sides sticks with algebraically summed inputs (1.4),
Uncoupled side sticks with algebraically summed inputs and disconnect switch (final A320 implementation) (1.8),
Uncoupled with algebraically summed inputs and priority logic (original A320 implementation) (3.3), and
Uncoupled side sticks with with algebraically summed inputs (3.4).
So, Airbus chose to implement the "second best" option (using a disconnect switch). The same article speculates that even though several sound alerts might have been triggered - including a sound alerting of "Dual Input" -, the stress situation makes them insufficient:
[...] in the circumstances identified as triggering instinctive responses the value of such alerts is degraded due to the inevitable attentional tunnelling that operators experience in high stress situations.