Why is this not a proper solution to handling transparency in deferred rendering?
PaulHK is right in what he said: you have to consider that there may be more than 2 transparent objects behind each other.

Also, the idea of deferred shading is to render the geometry only once to be more efficient. If you render the geometries multiple times, you lose (part of) your efficiency. Moreover, the lighting is deferred, thus you'd need to do lighting calculations for all your geometries before you can do the correct color calculations from transparency. So what you're really doing is going back to forward shading.

That being said, one solution is to first render any opaque geometry with deferred shading and afterwards render the transparent objects with forward shading, so maybe you weren't too far off. Those transparent objects however shouldn't be affected by too many lights to still render frames "fast".