This question has a strong relation with my other question: Isometric rendering without tiles, is that goal reachable?
I want to depth sort objects in an isometric world
You can do this with separate pre-rendered Depth-Maps for every object. With additional Normal-Maps you can simulate Deferred Lighting, too. But this technique requires 3D creation for every object to render diffuse, normal and depthmaps for correct intersecting objects.
See the XNA-Demo at https://www.youtube.com/watch?v=-Q6ISVaM5Ww
Every object in this demo is just a rendered sprite with diffuse, normal and depthmap.
At the end of the video you see how it works. The author has an additional explanation & shader code-examples in his blog at https://infictitious.blogspot.de/2012/09/25d-xna-rpg-engine-some-technical.html
I think the same is possible with WebGL, too.