I'm not sure about the details, but I do like the idea of obtaining seals. However, it will have to be balanced with provisioning/supply rewards (i.e., the equivalent of 3 seals for a piece of wood) or that content would be abandoned.

Also the battle phase would have to be balanced with Chocobo quests (or that content would be totally abandonded).

In essence:

A good hamlet run would get you up to 300 seals (perhaps an additional modifier based on hamlet level. So level 5 would get you 2.5x = 750 seals).

Turning in provisions would be equivalent to provisionin/supply (so, a militia bow for example would be about 10 seals, or 100 points = 1 seal). There could be a futher bonus for hamlet level, so at level 5 you would 2.5x = 25 seals for a bow.

Points should be permamently cummulative (but the only reward is 'achievements'). So you could get an achievement for 1,000,000,000 points.

This would all be on top of the present drop rate (and bonus drop). This gives the end result:
Lots of people would participate --- yaay, fun way to get seals.
Lots of people would be happy -- yaay, seals.
Some people would occassionaly be very happy -- yaaay, super rare drop item on top of seals!
It makes sense -- I think Hamlet Defense is supposed to be organized by the grand companies, so only makes sense they reward you.