The only reasonable way to do transparency is with (effectively) a 1 bit alpha channel, i.e. either on or off. To this end you'd use an alphaFunc in your shader to define the cutoff point (e.g. GT0 to make alpha 1-255 visible, LT128 for 0-127, GE128 for 128-255 or GE192 for 192-255). You'd still use an ordinary blendFunc as with normal solid shaders, I believe, since the alphaFunc takes care of transparency, so I don't think an explicit depthWrite is required.
This will only be visible ingame; ModView completely ignores shaders, but you can enable alpha blending in the menu (which is more akin to blendFunc GL_SRC_ALPHA GL_ONE_MINUS_SRC_ALPHA, with the same problems: there's no depth sorting, so you get visual glitches.)