I think the best way to prevent the problem you are suggesting is to play with a mature group of players who wouldn't try to take advantage of the system too much by making crazy spells that target Scholarship or whatever. Also it would be important to have a GM who is confident enough to resist them if they try it. In my original proposal I picked Discipline because it makes complete sense given the context. However, I agree that having the confidence that comes with training with a weapon could provide resistance too. So I will go with the second version of the spell which is a zone block against attacks that can be resisted by whatever skill the target is attacking with.
Let's say you only allow people to resist with...
Alertness, Athletics, Conviction (act of faith), discipline, empathy, endurance, fists, might, rapport, weapons, and maybe 1 or 2 other skills.
In a way this is even more problematic than any skill. With any skill being a potential defense, you really can't effectively defend, so you just pick whatever you like and the traditional defenses. With a select group like the above, you have now placed undo weight on those skills. Major Villains will need to be decent in all of them or they'll get struck with a lame attack they don't defend against well. Non-casters will just be at a major disadvantage against casters since they can't put up a Block. It would really kind of suck. The nice thing about a small number of defensive skills except for very, very rare things is that it leaves the players with a lot of room to express their character without feeling penalized by the mechanics. Same with the GM and expressing an NPC. I'm not against this sort of thing because I'm against spell creativity, but rather because I think it would damage a more fundamental creativity. Sure, everyone could put little straight-jackets on themselves and artificially restrict what spells characters use, but I don't think that's a very satisfying way to go for most groups.
That's why I tend to think the way that's more in the spirit of the rules (especially given the GM advice) is to use the default defenses, but if you can come up with something else to overcome an effect or defend then that's ok to use too. So Morgan's Earth spell cast on your Hercules-clone might prompt the player to go "Grargh, Hercules scoffs at the moving earth! I overpower it with my great strength!", and the GM might respond "sound good, roll might". Maybe against your fear spell someone might say "I don't believe this is real, I want to overcome this with my mind!" and the GM might let them counter the ability (kind of like a non-magical counterspell) using discipline. That encourages creativity but doesn't, imho, risk damaging the game at all.
I'll grant I tend to be pretty certain of my opinion a lot of the time. Unsurprisingly, perhaps, I do think I am right here. It might not be a problem in every game allowing this, but I think in a general sense it is problematic. Kind of like how 3E D&D Clerics aren't overwhelming powerhouses with every group, but the rules certainly allow a cleric to be such a powerhouse.*
*Hence the 3.XE term CoDzilla (Cleric or Druid - zilla).