One idea is to have an entry field for strings of characters that must be treated as single characters. Using Zompist's SCA, I've often found myself resorting to such extravagant representations as Devanagari characters for phonemes that the Latin alphabet has trouble representing easily.

This SCA could set aside a block of rarely-used Unicode characters- say, Yi syllabics- and replace each string in this block with a character from this block. (The nice thing about computer programs is that they can automatically replace and read characters that humans can't easily type or interpret). It will do the same with strings in the rule file as it runs. Then, at the end, it converts them all back. You're still working with one phoneme = one character, but the human doesn't have to mess around with special symbols.