The molecules themselves are randomly oriented. Bonds are broken by the correct frequency of light(E) on particular bonds, not the whole molecule. The interaction of light with the whole molecule, which is involved in circular polarization, does not break bonds. Any freauency of circularly polarized light is effected, by D, or L molecules. Either the light passes, or it's reflected. It will either give the molecule some angular momentum, or give it some linear momentum. In either case if the amplitude of the wave is sufficient that the momentum results in bond breaking, the temperature is high enough that no difference in destruction of either D, or L will be notable.
"One might as well assert that inserting a screw into a threaded hole will have the same result whether the screw thread direction is the same as, or opposite to, the hole thread direction."
The light either passes, or it is reflected.
Also, the proteins didn't come from space.
As I understand it, it is the amino acids which are chiral.
The molecules themselves are randomly oriented.... no difference in destruction of either D, or L will be notable.
As to this point, it seems to me that, if it were a correct argument, then a handed molecule in solution would have no effect on the polarization of transmitted light (because the orientations wrt the light would be random). But this article specifically mentions the effect of solutions of chiral molecules on light polarization so I think your argument is wrong.
Off the cuff I can think of two ways it may be wrong. First, the orientations might not be random (e.g. a magnetic field migh align them). Second, you have considered the bond as if it were isolated but it is part of a larger quantum system and it is that structure that affects the interaction of the bond with light. For example, consider a helical structure and suppose that the interaction is significant only when the structure is aligned in the propagation direction of the light. Even if you rotate (not reflect) the helix 180 so that it's facing "the other way," it will look the same to the light and so have the same rather than an opposite effect on the light.