In reference to #3, IIRC, there is some kind of counter that registers transgressions against an ally. When a certain threshold is reached, your ally will break the alliance. In my experience, I could get away with assassinating emissaries from an allied clan. But killing some low-level generals often resulted in a breaking of the alliance. Only stands to reason, no? But I could be wrong about the counter.

The best counter to geisha, as has been mentioned, are mid-high level ninja. Level 4 would be minimum to have a reasonable chance of success, lvl 5 or 6 will almost always succeed (provided the geisha is low level). You can throw a swarm of low-level ninja at her, but your Daimyo/heir/taisho might be dead before you succeed. You can delay a lower level geisha by flooding the province you wish to protect with shinobi (at least 6, but 8-10 is better). She will eventually get her target if you don't kill her, but at least she will have to wait some number of turns until 'a more suitable time.'

As to #1, Asai pretty much said all there is to about that.