Answers to big questions in one clump:
Godspark and detect magic - Actually, Halgo's kind of set for this.
One, I keep psionics and magic as relatively seperate entities (although they were once, and may be again, rejoined), so the psionic characters aren't going to notice.
Two, to my shame, Capellan had thought through keeping the stone a secret much further than I had. For the next two sessions, whenever Detect MAgic was needed, Halgo was first to offer a casting using the excuse "Save it, we may need you to trade that spell out later and I've got them to spare" if any other party members looked like they were getting ready to cast it. Then, when they hit civilisation, Halgo got someone to make a lead-lined chest he could keep the god-spark in, and it isn't until he asked how much it would cost that I worked out what he was doing.
So, end result, he's safe from most casual magical attention. Of course, the Ki'Rath have been known to make some money through the sale of information, so it's not like he's the only person in on his little secret....
Yips and other organisations
I'm not to worried about this. For starters, the good churches aren't going to be all that keen to strip another race, even kobolds, of their right to individuality and choice. The Lawful Good ones can't argue that the ends justify the means, and the Chaotic and Neutral Good churches are going to be appaled - one of the reasons the Yip monks were a closely guarded secret until the Trollmist Wars and casualties in trapped goblin caves lead the Church of St Cuthbert into using them openly as part of the military. Since then, there has been a lot of pressure on the pragmatic Cuthertites to free the Yips. Assuming the Copperheads ever actually get back to civilisation, we'll start to see the impact of this. Bor is just a little to far afield for political mechanations of the empire to have impact.
Evil churches may run with the idea, or already have something similar.
The demon-worshipping Guantians have rat-men, which are trained in stealth and assasination rather than monkish arts, but they make a rough equivelent.
Hextorites will likely regard the kobolds as too weak and pointless to train, but will likely start monkish orders based on stronger creatures that breed fast. Orcs, maybe. Or trolls and ogres
The Settites to the Empire's west have their own breed of kobold tribes to recruit from, kobolds descended from snakes rather than dragons. Again, they don't have a monkish focus, but they do exist in large enough numbers to serve as a counter point to the Yips...