No longer can I say that the topic of allergenic extraterrestrial life hasn't been taken on in science fiction. Patrick Neilsen Hayden of Electrolite, who is certainly in a professional position to know, passes on the word that the 1999 novel BIOS (by Robert Charles Wilson, reviewed) includes this very idea.
On a related topic, a number of old sf stories made use of the chirality of amino acids and the resulting proteins, with a plot point usually being the possiblity of starvation when trapped in an environment full of the wrong-handed food source. Given that such enantiomeric compounds can have very different properties in the body, I'd think that such an environment would not only be non-nutritious, but extremely toxic.
But are there any such places (stipulating an abudance of life-as-we-know-it in the universe to make it more possible)? That gets right into the question of how we ended up with only L-amino acids (and only D-sugars, which get less attention, undeservedly.)
There are plenty of theories. One thing that most everyone agrees on is that what we see now is a founder's effect - life got started with the series that we know, and stuck with it ever since, across billions of years. (Reminds me of Microsoft.) But was it a pure 50/50 chance at the beginning, or was the deck stacked? For that to happen, you have to have a chiral environment somewhere for it to develop.
Explanations such as seeding by meteorites containing chiral amino acids (or planetary formation from a cloud containing a chiral mix of compounds) just push the question back a bit. Where did those excesses come from? I should note that a paper on the amino acid ratios in the Murchison meteorite was just presented at the same meeting that Jay Manifold has been reporting from over at "A Voyage to Arcturus." Maybe he can give us a report.
For some years, the explanation that was hauled out invoked the weak nuclear force, which is the first place you can find symmetry breaking down in the laws of physics. Trouble is, that's such a small effect on the thermodynamics (if there's an effect at all!) that it's really like sticking with the 50/50 chance.
Another interesting idea was that circularly polarized radiation, potentially from neutron stars, preferentially breaks down one enantiomer of simple molecules over another. This still doesn't give you much of an edge, but it's a lot more compelling explanation that the weak nuclear force.
Last year a theory was proposed that formation of simple biomolecules on rock surfaces (a hot topic in origin-of-life research) might have something to do with it. Calcite seems to absorb different enantiomers on different faces of its crystals, which could have led to local excesses - too local, some say - of one enantiomer. If one of these microenvironments was the first to start things on the road to life, though, that would be all you need. It's still another form of 50/50 chance, depending on what crystal face you pick, but at least (as with polarized radiation) you have a semi-plausible mechanism for generating an excess of one chiral form.
These ideas and others are discussed on this site, but note: that page also brings up an experiment from a few years ago that suggested that magnetic fields could induce chiral chemistry. This result has since been throroughly discredited. No one could ever reproduce it, and it turned out that one of the original graduate students faked the results. Not a smart career move, considering how much interest (and scepticism) the first report got.