Your problem will solve rendering with 1bit alpha. Which means you specify some alpha of source texture which is not rendered (mostly 0.5).
You have to write your own shader for saving depth from light and use instruction
discard. Discard exists in hlsl, glsl and in cg as well. It exists only in pixel/fragment shader and discards curent fragment from the rendering into backBuffer and into z-buffer.
if (texSample.a < 0.5)
Advantage is that you don't need to change yours 2nd pass rendering, only rendering of light's depth. Also i have prove that it works:
If you want to render correct shadows for multiple transparent objects you will have to use multiple depth textures, with depth and opacity information rendered using depth peeling. And for smoke, hair etc. Deep opacity or Fourier opacity maps are best solution (I mostly recommend Fourier opacity maps)
edit: I just realized that i forgotten to add credits. As always. The tree model is from loopix project which is just great if you are looking for some lowpoly, one texture and free models of vegetation.