Proposed:
if you are L, you can attack neutral monsters that are C without an alignment hit [this could be extended to NL, to mesh with NC below]
if you are N, you can attack neutral monsters that are C or L without an alignment hit
if you are C, you can attack any neutral monster without an alignment hit [this could be extended to NC, making for more interesting gameplay]

I think this helps solve a lot of the current issue, on its own--though it needs a little tweaking here or there (once you've injured something, it cannot suddenly not notice you, for instance [at least, I think I saw this happen]. a few other changes, as well). I also think it makes a lot of thematic sense (in fact, it is partially based on mechanics for Paladin boost) and meshes with the gods well. In addition, I think it offers a little more interesting gameplay, since *by far* the easiest way of getting to C- [or C, if NC is used above] is now non-existent, forcing the player to find another way--perhaps having to kill Twyat Pare. [well, I guess farmers & beggars would also work since I think they have an intrinsic alignment hit, but maybe that could be cut a little for C characters. maybe a further suggestion].