For all the complaints about the alpha sorting glitch in SL, the fact remains that SL actually handles alpha sorting FAR better than most other 3D apps do, including the majority of video games. As I said earlier, the only reason you don't see it in games is because professional game artists go to whatever lengths are necessary to build around it.
That said, yes, it COULD be made better, as Argent said. But to do so would, in all likelihood, carry some serious drawbacks:
First, the more sophisticated you make the system that figures out the draw order, the slower it will operate. There's no way around that under the current standards for how graphics pipelines work.
For example, Maya has an option for advanced transparency sorting, which generally does a really good job of making sure things are drawn in the right order. But when it's enabled in any but the simplest of scenes, frame rates drop considerably. Consider the already low frame rates SL operates at on most computers, factor in that the average scene in SL tends to be far more complex than a typical working scene in a traditional 3D modeling program like Maya, and any attempt at employing a similar system in SL would be a recipe for disaster. It just wouldn't be able to operate at any semblance of speed.
Once real-time raytracing starts to be come the norm, as opposed to traditional rasterization techniques, a lot of things will change, including transparency sorting. But we're still several years away from that. Significant changes to hardware standards need to be adopted first, and that's going to take time.
Second, the glitch has been such an inherent part of 3D graphics for so long, techniques have evolved to take advantage of it, rather than simply hide from it. Certain objects and effects like trees, plants, fire, chandeliers, etc., are commonly created to capitalize on the glitch, to the benefit of geometric simplicity. Were the glitch to be "fixed" tomorrow, a lot of existing content would break.
That's not to say that we should hold on to old techniques forever, of course. Certainly as technology evolves, we do need to evolve ourselves along with it. But all perspectives (no pun intended) should be fully understood and fully considered before deciding what's a "fix" and what's not. To solve one problem by creating another is not necessarily a good decision (or a bad one).
Bottom line, alpha sorting is a minor annoyance in SL, and will continue to be for the foreseeable future. Even if you do all the right things to work around it, just like the pros do, your neighbor might not, and then your build will be screwed up anyway. All we can do is deal with situations as they arise, and employ the best solutions we can. Sometimes that means we can't design things quite the way we want them. Frustrating as that may be, it's just part of the SL experience. It is what it is.
Bodhisatva, I'm not quite sure what you meant by "separate walls", but it sounds like you're on the right track. If your current design isn't workable, redesign. It's often a good idea to make a 24-bit version of every 32-bit texture, and then break a wall into sections. Keep as much of it opaque as you possibly can by using the 24-bit version, and then use the 32-bit version only for the section(s) that absolutely need transparency. That could mean making a wall out of two or three prims instead of just one, but generally it's worth the investment.
Another option is to "insulate" a wall by hiding opaque prims inside partially transparent ones.
There are lots of possibilities. Employ a little creative problem solving, and I'm sure you'll be able to glitch-proof your build just fine.

By the way, Argent, how certain are you that a change actually was made with Windlight? I never noticed any difference, myself, between how Windilight and pre-Windlight viewers handle alpha sorting. Perhaps I'm just not observant enough, but as far as I could tell, nothing changed in that regard.
I've always just chalked up the claims of "alpha sorting is worse with Windlight" to the rantings of the small but vocal "everything's worse with Windlight" crowd. As you're not a member of that group, I'd love to hear more about your assessment of what actually did change, and what didn't.