From my experience the only way to hook a small fish deep is to either have a really unexperienced angler or to not be using a bobber. If you use a bobber and set the hook when it goes down you should never get a hook in a BG that bad. If you can't use a bobber then just keep a nice tight line....dont let the fish run like you would a big cat or carp.
You may also try fly fishing for gills. It's really fun especially when you get some nice sized ones on and I really doubt you could let the hook get too deep on them.
One question I have is are you using live baits or some type of artificial? Also what depth are you fishing at? Deeper water means that it will be harder to detect the bite, especially on smaller fish.
