The simple thing to do would be to not allow those type of magics to be in the game. Why have Chameleon, Invisibility, Detect Life, etc in the game if it's going to be abused.
I think what I would do is just not allow you to enchant with those types of magic. Just limit it to Fire, Frost and Lighting Damage, Shield, and a couple more magic effects.
I'll repeat myself, why? Why would you willingly take out an aspect that many people find great fun, instead of simply choosing not to use it yourself? How is this concept hard to comprehend? It is a single player game, that means that what you do in your game has no possible way of affecting anyone else, and that goes both ways.
Why do you care how others play their game? Mind your own business and let others do the same.
I thought Fable 3 handled this aspect quite well. They should make your weapons and enchantments grow overtime & have objective based upgrades: Kill 1,001 Spriggans near Riverrim, Make 15 greybeards love you, Drag 84 Bosmer villagers to work, Successfully complete 30 quests, Have an orgy with 4 other people, Find all 50 gnomes, etc...
Let me start by saying, I don't hate Fable. I'm an advlt and I'm able to see positives and negatives in any game and base my decision around that. Fable did many things well, and many things poorly. Anyway, to my point.
I think Fable 3 handled this aspect quite badly. Forcing me to complete arbitrary tasks to improve my weapons is not an engaging or rewarding way to design a game. When the game asks me to go out of my way to farm a certain creature for hours just to make my sword a little better, I'm not going to do it. I don't find that fun and I won't waste my leisure time doing something I don't enjoy. It's the same reason I don't do a lot of daily quests in WoW, they can be well designed quests, but the repetition takes the fun out of it eventually, and I'm not going to bother, unless there's something amazing waiting for me once I've done it a certain number of times.
And incredibly cool reward will make me do something that's reptetive or boring, only because I will be incredibly satisfied once I get that reward and gradually counting down towards it is it's own kind of fun. But the bonuses in Fable 3 weren't worth the effort at all. That game is incredibly easy already, why work to get a reward that doesn't matter? I was plowing through the game as a living god, utterly destroying anything that looked at me wrong, why would I want to do tedious tasks that pull me away from the action just to get a slight bonus that ultimately doesn't affect me?
No, Fable 3 handled this badly, it pulled focus from the good parts of the game, which is something you never want to do. If you make a game, make it as good as it can be in every respect. If a part of a game is not engaging and satisfying you do not pull focus towards it and you absolutely do not force the player to do it. If a system doesn't work well, you improve it, if you can't do that then remove it. Never force the player to go out of his way to do something that is not fun. If a game is not fun to play, I'm not going to play it. To use a food anology (Been a while since I did) I will not eat at McDonalds if I have the option to have a nice steak dinner instead.