Hi, nice of you to finally join us!
To answer your points in order:
You don't need to kill civilians, but if the civilians don't want to use their skills they aren't likely to use their skills well. You can get ramen by coercion, but it'll be overcooked, undersalted (salt's valuable, yo), and that yellowish water is probably piss, to use the example from the chapter.
Next, if you're poor and have a family you're not likely to have the skills to produce a house that a ninja would want to live in. Remember that this is not the modern age, but rather the medieval times, where dirt houses were pretty reasonable, all things considered, and the cities were basically wooden and thatch firetraps. No self respecting ninja particularly wants to live among the filth, so they need highly qualified workers to do build a manor worthy of a ninja, and those highly qualified workers are likely part of the manor construction guild who are likely part of the Merchant's Council.
If that council wants you to stop, but you're poor and are going to do it anyway, you can't hire the ninja to protect you since you are poor, and the Merchant's Council is likely to have its constituent guilds make sure you can't buy food or get your clothes fixed or show up to work, etc.
If producer x of iron doesn't want to trade with me, I'm kinda shit outta luck. All the business in the area is regulated under these guilds, so all the iron producers and weapon producers are not going to sell to me because they're all part of a guild, unless I want to depend on a foreign nation for my weapon supply, which should be exactly as appealing as it sounds.
That is true; establishing cartels takes tons of coordination and power. However, in this age there isn't many people to control in order to have an effective cartel, so you could. However, try to use the ninja's power in any sort of directly threatening manner and suddenly you find everyone skilled getting the hell out of your village.
Increased productivity doesn't have to be zero sum for there not to be bad effects as a whole for the guildmembers. You don't need a machine that can do one man's job to replace nine tenths of your workforce; you just need a machine that can help one man do the job of twenty. And ninja are very good at doing the job of fifty civilians. Ninja are much more productive, yes, but not highly numerous and certainly not enough to maintain their current level of technological development.
As for something shady going on behind the scenes, may I introduce to you the Watchers?
Anyway, your objections are all pretty reasonable if not for the time period, and certainly the Industrial Revolution is going to throw this entire system down the gutters, but for now it'll keep our hypothetical earlier ninja optimizers from running the market so hard that we'd never be able to fit in.