1.) I believe I've heard the verb "to founder" used to describe a ship which is just begining to sink. A Negotiatiated peace would be one achieved through discussions and compromises in terms, rather than through bloodshed. The work being done toward this objective began to look as if it would fail completely.
2.) The verb "to sow" means to plant seeds. ("As ye sow, so shall ye reap.") This is a metaphor, suggesting the government has planted seeds that will grow into chaos, or a complete lack of organization and order. I suppose the implication is that the rebel groups were organized to some extent, and now even this semblance of order will be gone. That is, weakening the rebels will lead to an organizational vacuum.