I normally use artificials for halibut, which eliminates both of your problems, but generally if you hook a fish deep it's better to cut the hook and let it rust out, than ripping it's stomach apart trying to get the hook out. As for setting the hook, try a trap rig on your anchovies. Halibut seem to be pretty good at staying away from the heads of baits and can be hard to hook sometimes. I'd definitely suggest giving the artificials a try, especially if you do a lot catch and release, or catch shorts fairly frequently (such as inshore float tubing). Lures make it much easier and safer to release fish, not to mention how much funner and more gratifying it is than bait fishing. Check out the article on the saltwater section, or post questions here if you'd like to get in on that, the guys on this board are some of the best when it comes to halibut on artificials.
-Brian