Ultimately, I had hoped to build an alphabetical index of domains by which the gods could be referred. However, I realized how nearly impossible that task could be (possibly taking longer than laying out the whole book, if you can believe that). For example, for Erik Tenkar's Pandantilus, Lord of the Privy and Patron of Gong Farmers and Muck Rackers, I suppose I could create entries for "privy," "gong farmers," and "muck rakers," but that doesn't even begin to help DM's who might be looking for "feces" or something similar. Hell, even "gong farmer" can be "gongfermor," "gongfermour," "gong-fayer," "gong-fower" or even "gong scourer." Also, since the domain of so many of the petty gods are quite inclusive, building an exhaustive list would require re-reading each of the 315+ petty gods entries, adding a who-knows-how-long list of associated words, and trying to build the index from that. This is why building an alphabetical index by topic that would be truly useful seems to be near impossible (from my POV).
So I've made an executive decision. I've laid the index out alphabetically, with the gods' names, domains (as listed in each entry's header), alignment, affiliations (pantheons/cults), and page number. The entire section is 9 pages long. I think that's short enough for DM's to peruse in a few minutes and find a petty god that may fit their needs, but complete enough to actually be useful.
Even building this index still took several hours. Imagine how long it would have taken to build the other one.