There is a unicode equivalent to "dha": à U+0927 This is not for roman script, but for devangari.
I think the obvious thing to do if you want to sort in the Pali/Sanskrit alphabetical (alphabetical is not quite the right word here) order is having in the records for the words in your computer a field with the word written in devangari script, even if you don't intend to print that field when you make the hardcopy of the book.
