I got a negative score once in my current playthrough. It didn't bother me much. Certainly it didn't bother me as much as in the next month, when a country adopted the zero-tolerance policy.
I don't think you need to add more early-game missions.
Actually, I'm wondering if maybe the early game missions open up too many research options. In my current game, I still haven't got the Bonaventura; but I do have some pretty advanced tech, and a seemingly endless amount of research opportunities. From early missions and landings, I've got guild and academy engineers, guild rep, church matron, and stacks of different low ranking captures. I even managed to capture an ESPer who happened to be standing right outside my ship at the start of a progrom. I've seen cruisers land - but decided not to try to take them on yet. I'm starting to think that I could probably win the game without ever shooting down a single ship!
Maybe that's all fine; but I'm not deliberately trying to play the no-shooting-down-ships strategy. It's just happening because all these other resources are presenting themselves to me. And I'm a bit worried that I'll leap-frog over most of the air game by getting advanced ship tech before I get basic ship tech.
As I said, I still don't have the Bonnie, and I'm not sure what I need to research to get it. I can however research fighter construction and heavy attack craft... so I don't have a shortage of ships as such.
[edit]
To clarify, I'm not trying to suggest that something should be changed. I'm just sharing my thoughts and experiences. I'm not dissatisfied with how my playthrough is going, and I expect that other playthrough will be different and interesting in other ways.