Shhhhhhh I was deliberatly ignoring that 
Any SG which allows such an effect to be cast without God saying, "Um, no. Bad magus. To Hell with you," deserves to have their saga ended.
At this point, the saga is likely over, so it's really moot...
Ending the saga is the point of spell.
The reason why this rule (ArM5 p. 85) is incredibly stupid is that general resistance vs the other realms is a game mechanic that was used from ArM1 to ArM4 and for all other occasions other than Faerie/Magic powers granting resistance to humans other than PM. The ArM5 setting deviates from a general mechanic in order to make the PM special - that is not special but working as the game mechanics should. Imagine a rule that said that all dice rolls in the game should be done with D10 except when you ride a horse. When you ride a horse you have to use a D6. Why? Well, the game creators wanted to make stirrups powerful so when you ride with stirrups you can roll the usual D10. If you think that such a rule is good then I have nothing more to say.
Jakob, you are looking at this backwards. Having magic resistance that requires spells or other effects to penetrate is an exception, not a general rule. To affect something with a Might Score, you have to penetrate. To affect someone with True Faith, you have to penetrate, and to affect someone with Parma Magica, you need to penetrate. But normally, you don't need to penetrate to cast a spell on someone. You seem to wish that this exception was more widespread.
From what I can find on the internet, The Stormbringer is a 3rd edition adventure, with a 4th edition sequel. I am not sure exactly how the Stormbringer worked, but I suspect that treating him as a formally human creature that through Mystery Cult type initiation transformed himself into a Might based creature linked either with Faerie or the Infernal.
Also, the rule about MR isn't so much arbitrary as it is a setting dependent one.
In previous editions of the game, all of the fluff about Parma Magica being a major breakthrough in Magical Theory was sorely undermined by the fact that everyone and their dog exhibited MR of some sort or another. Granted, a huge part of Parma's effectiveness is that it blocks the effects of The Gift while possession of Might doesn't necessarily, but I believe the point stands...
Well, in the OP's defense one should also say that some Infernal and Divine methods and powers give you magic resistance ("true generic" magic resistance, rather than partial protection from some form of magic).
Anyone who is any real threat needs magic resistance. At least if they are going to go face to face against a magus. Sure the amazons could bombard a magus from their island. A Sahir could unleash a jinn swarm. Or whatever. The thing is, it basically makes it so enemy sorcerers are either a) magi, a fairly rare event if the Order hasn't torn itself to bits, or b) inhuman. Yeah, there are infernal buggers, and Divine buggers, but that means either baby eaters or guys with God on their side. Not a lot of variation there.
It means you have trouble with any credible human threat to the Order from outside. Any major Divine or Infernal force stops being human and is really just demons or God. The setting choice is basically "the Order is all powerful compared to other humans." The magi just aren't better, they make it so the only credible human threats have to do it by artillery strikes. (Which to be fair make for great horror stories.)
Or sneak attacks.
There's a lot of damage to be done if you can knock down an Aegis and then attack immediately thereafter with either unresistable or highly penetrating weapons.
Sure, you're not going to be getting the strongest covenants that way, but it'll cause havoc and possibly give you the chance to learn, and spread, the Parma Magica before they can work out where to strike back at.
Another option would be a hedge tradition making a breakthrough and developing magic resistance akin to hermetic Form Resistance. That would be a major upset, even without the Parma Magica to back it up.
Actually the thing that bugs me the most about the Parma situation is on page 16,
Really? If you are afraid of God getting mad if you mix it up with the Church, I would be doubly scared about mixing it up with people who have True Faith. And recruiting the guy with infernal resistance? Well, I can think of some worse choices, but they involve blowing up the planet. And the Parma person? I think the proper plan for them is interrogate them, THEN maybe recruit them. I mean, if a guy has stolen Parma you might not want to recruit him and give full access to all your secrets.
Shoot first and ask questions latter.
Yeah, that would be a good policy. Okay, you might annoy God every once in a while, but it shouldn't be too bad. However the "join" part seems to me like "Here is my back, here is a knife, have fun."
Kill them all and let God sort them out.
Also, "Join or Die" is what you say when you are trying to be nice to the guy. No one said you even have to give them the option. See how enlightened Flambeau was?
The policy is Join or Die. It says absolutely nothing about which option is presented to the individual. 
Also, I feel it should be pointed out that there are, at least theoretically, other ways to acquire general magic resistance than stealing the secrets of Parma Magica from the OoH. It would likely require a magical prodigy of the same calibre as Bonisagus to develop it, of course, but I'd argue that's a good enough reason to recruit him or her right there.
Furthermore, 'Join or Die' hasn't proven a very good recruiting tool - Flambeau himself failed to secure Varstus' membership by that stratagem after all and the policy proved disastrous during the Order of Hermes' expansion into the Hibernia Tribunal...
Columbae from HoH:Soc. Quite well equipped to pull this off to some extant even at relatively low levels.
I agree this is a problem, at least when creating threats to the Order in general. Or, when threatening a large group of experienced Magi. Story Guides do have more options when creating threats for specific Magi. Most Magi are specialists so custom opponents with a few well chosen virtues can become quite a problem. It doesn't matter how high your CrIg mavens penetration is if the the knight trying to cut his head off is immune to fire.
I generally avoid threatening a large group of experienced magi and magae. 
My threats to the Order are threats from within. The Order as written also seems to present itself (to me) as complacent and no longer in expansion. All of the Tribunals presented in the books have histories that seem to stretch back nearly to the founding of the Order. I haven't reviewed The Contested Isle's Hermetic Timeline. So I get the sense that the Order exploded onto the scene, occupied the known world, and then just as suddenly stopped.
You are living in a 5th edition world where Flambeau was a pc wuss and foppish dandy. I play in a 4th edition world with 5th ed rules, where Flambeau is still manly and brave.