I am with Never-ending winter regarding assigning level to non-hermetic magical effect: take the Ease factor.
As it was pointed out, to dispel an on-going effect, you need to know what type of effect it is: which realm it belongs to, which form (in case of hermetic magic) or at least which type of effect it is (entrancement, hex, curse...).
Without this information, it is a bit like trying to quench an fire without knowing its origin: let's pour water on this metal (or oil) fire and see what happens.
So he will need to design a whole set of InVi set to identify the source of power (at least Faerie, Magic and Infernal, I hope he won't try dispelling Divine effect... onthe other hand ...). Then if you are lenient, you might let him try a Realm Lore check to identify the spell so he can finally try to dispel the effect.
Now, if you talk about countering a magical effect, he has to do all that in a fraction of a time, so unlikely. Yet again, he can still try to fast cast a PeVi against magical realm: Curse and hope he hit the nail on the head. Except that the edgie was using an Faerie/entracement power.
Since Edge magician, diabolist and so do not have a systematic and formulaic ways to trigger their power, it is nearly impossible except for people of the same tradition to identify which powers they are using when they point their right hand ring finger toward you when blinking with their left eye.
Now, also give to the player an opportunity to shine: if he knows what he is up against, he has done his homework on gathering intel against said Edgie The Baddie III, he knows that he is drawing his power from the Magical realm and his rumored to be able to Curse people and Shapeshift, then he has a fair chance when he will spont his PeVi to know he need to dispel a Curse and go straight for it. Edgie the Baddie III will soon be defunct. And it is normal: for me, there is nothing more powerful than an Hermetic magus who had time to be prepared.
The way you need to present the situation to the player would be the following:
- Acknowledge that PeVi is the most versatile way to dispel any supernatural powers;
- Remind him that even to dispel Hermetic magic, he need to know at least the form of the spell he is trying to dispel/counter other wise you will apply the guideline of Wind of the Mundane silence
- Propose him a list of spell he would need to develop to assist in his quest of becoming an efficient witch hunter (InVi: Perception of the Extraordinary Thread, which allow to detect which Realm is Powering the effect he wants to dispell; then a set of InVi per Realm which would be the equivalent of Sight of the Active Magic)
- Suggested him set of competences that will help him (Realm Lore, Area Lore)
- After one suggesful witch hunt which was a much closer call thant expected, have him meet a "professional" with hunter (either another hermetic magus, or even better a priest exorcist (at least somebody outside of the Order), which reckon his ability and willingness to hunt evil-doer and although does not share his philosophy would like to recruit him or train him because he is pragmatic and needs any ally he can find);
- You can also mention to him rumour about a Mystery Cult which seems to gather exorcist, witch hunter, nightstalker and such, which documents all sorts of supernatural powers, threats and ways to neutralise them, with the possibility to be initiated in some relevant virtue (Detect Holy/Unholy; possibly even Comprehend Magic from the Pralixian, or Ward techniques).
The point is not kill his character concept, but make him understand than generic PeVi is like using a shotgun to kill a fly: very ineffective. There is a reason why there is no PeVi spell called: Dispel Every-Any-All, because hermetic magic cannot do it, the effect would be too diluted. Use the example of Wind of Mundane Silence needing to beat twice the level of the hermetic spell the magus want to dispel to illustrate that, so it will be even worse for non-hermetic effect, and impossible for other Realm-aligned power.
By providing an explanation (based on RAW), proposing ways for his character to achieve his long term goal and enticing him with interesting story hooks, he should not feel cheated.