I have been working on an area lighting implementation in WebGL similar to this demo:
http://threejs.org/examples/webgldeferred_arealights.html
The above imp
The good news is there is a solution; but first the bad news.
Your approach of using the point that maximizes the dot product is fundamentally flawed, and not physically plausible.
In your first illustration above, suppose that your area light consisted of only the left half.
The "purple" point -- the one that maximizes the dot-product for the left half -- is the same as the point that maximizes the dot-product for both halves combined.
Therefore, if one were to use your proposed solution, one would conclude that the left half of the area light emits the same radiation as the entire light. Obviously, that is impossible.
The solution for computing the total amount of light that the area light casts on a given point is rather complicated, but for reference, you can find an explanation in the 1994 paper The Irradiance Jacobian for Partially Occluded Polyhedral Sources here.
I suggest you look at Figure 1, and a few paragraphs of Section 1.2 -- and then stop. :-)
To make it easy, I have coded a very simple shader that implements the solution using the three.js WebGLRenderer -- not the deferred one.
EDIT: Here is an updated fiddle: http://jsfiddle.net/hh74z2ft/1/

The core of the fragment shader is quite simple
// direction vectors from point to area light corners
for( int i = 0; i < NVERTS; i ++ ) {
lPosition[ i ] = viewMatrix * lightMatrixWorld * vec4( lightverts[ i ], 1.0 ); // in camera space
lVector[ i ] = normalize( lPosition[ i ].xyz + vViewPosition.xyz ); // dir from vertex to areaLight
}
// vector irradiance at point
vec3 lightVec = vec3( 0.0 );
for( int i = 0; i < NVERTS; i ++ ) {
vec3 v0 = lVector[ i ];
vec3 v1 = lVector[ int( mod( float( i + 1 ), float( NVERTS ) ) ) ]; // ugh...
lightVec += acos( dot( v0, v1 ) ) * normalize( cross( v0, v1 ) );
}
// irradiance factor at point
float factor = max( dot( lightVec, normal ), 0.0 ) / ( 2.0 * 3.14159265 );
More Good News:
Caveats:
WebGLRenderer does not support area lights, you can't "add the light to the scene" and expect it to work. This is why I pass all necessary data into the custom shader. ( WebGLDeferredRenderer does support area lights, of course. )three.js r.73