1. I wasn't suggesting peace time bonuses; I just think that combat bonuses make conquest too easy. I think any economic bonuses granted by Honor and Autocracy should be attached to warfare, or should help to mitigate some of the economic costs of warfare.
2. Gödel only proved that there are unprovable statements in mathematics. This doesn't make math any less viable an approach to balancing a game like Civ 5, and given that everything in Civ 5 is modeled using numbers, it is the best approach.
3. I agree with Thal and Soverayne that the unit-killing rewards aren't as big compared to other bonuses as you seem to think.
4. In my experience, Commerce is way more helpful than Honor in increasing my gold reserves. However, I think game speed may heavily affect the balance of SoW, since the bonuses are based only on unit strength. On epic speed (which I play), the bonuses don't feel as big since everything costs more, but I can definitely see how on standard speed the bonuses could be too big.
5. Maybe instead of attaching gold to unit strength, Thal should attach it to unit cost, which scales with game speed. I think this would also slow down the late game increase in SoW yields, since cost doesn't increase quite as fast as strength (correct me if I'm wrong).