Trout and char (brook trout are char), like most fish, have what is called indeterminate growth. Given plenty of food, protection from predators and suitable habitat, they will grow very large very quickly, stopping only when the physiological limitations of their body configurations will allow no more. At this point, they die. With largemouth bass, this is why the world record largemouth bass has peaked between 20 and 25 pounds with the most recent records all being egg-filled females.
Stunted growth, which has that big head syndrome you described, relates to a lack of food, or in certain instances involving trout, a failure of the fish to make the transition from eating insects and other low-calorie/high effort foods to eating minnows and crayfish, which are high effort by even higher calorie foods. Dr. Bob Bachman, who served as Maryland's head of cold water fisheries for several years, did his graduate work in Pennsylvania and documented this failure-to-switch phenomenon.
Anyhow, in your case, if the brookies are able to spawn in your pond, I'd venture the water is very clear, the bottom gravel very clean and the year-round temperature relatively cold. These provide ideal habitat for brook trout, but not so much for the food they eat. There's a good chance they'd eat whatever they can catch, be it bugs, minnows, crayfish or even mice.
Further complicating the issue is an as yet undocumented element attributed to the brook trout life cycle south of Maine and Labrador. Fred Mather, a pioneer in the field of raising trout and other fish in hatcheries and the fellow to whom Friedrich Karl Gustav Felix von Behr gave the first in North America shipment of brown trout, wrote a lot about raising brook trout in hatcheries.
He made the claim that Seth Green, another fish culture pioneer, was responsible for selectively breeding a short-lived strain of brook trout that has come to dominate the waters of the eastern U.S. What you need to know about this story is it is suspect because Mather did not get along with Green. Mather thought Green was a glory hound; Mather could be similarly described, but he never achieved the public acclaim of Green in the late 1800s when they were both doing similar work.
Anyhow, the story goes that Green selectively bred a strain of brook trout that, when well fed, will grow to three pounds within three years. Unfortunately, they die at the end of their third year. Green's acclaim, Mather hints, resulted in these brook trout being widely stocked and supplanting strains of longer-living brook trout that may or may not have grown as quickly.
It turns out, regardless of whether Green is the culprit, many strains of Eastern brook trout only live three or four years. This may, however, be not so much the result of selective breeding but because of the physiological strains of an arctic species having to survive the hot summers of the Appalachian Mountains. Or maybe some other factor. Keep in mind that pink salmon have a natural two-year life cycle and they only grow to between three and five pounds.
The buzzword in brook trout fisheries management these days is heritage-strains. If you do a google search on "heritage strain brook trout," especially in quotation marks, you'll turn up a lot of fish-nerd research.
As for your problem, I'd have to echo the thoughts of the fellow who observed that a 12-inch wild brook trout is about as good as it gets in these parts. Heck, I caught one about 13 inches last summer at Boiling Springs that was clearly a stocked fish and it was as big a brook trout as I have caught in 20 years. I was tickled to be able to land it.
It might not hurt to thin the herd a little bit, as you suggest, but the minute you start messing with he balance of a pond with the rare ability to support a still water breeding population of brook trout, you run the risk of destroying something good, even as you were trying to make it better.
If it were me, I'd say the perfect is the enemy of the good and leave the good thing you have to perpetuate itself!
