I too have a problem with the way the Ex Miscellaneae benefit works, for the reasons stated below. But first, I would suggest a house rule:

Open up the free major virtue to hermetic as well as non-hermetic. Open up the free minor virtue to supernatural and certain genereal virtues as well as hermetic. Disallow certain virtues I mention below for the reasons stated (generally that they are tied into hermetic magic as opposed to an outside tradition worked in).

The reason? Well, on each change:

1) Allowing hermetic virtue as a free major virtue- There are three that just scream being appropriate to the house: Diedne magic (Ex Misellaneae being the most likely house to hide in), elemental magic (well I always thought of it that way), and life-linked magical focus. I see certain virtues as being nuetral- they work for Ex Misellanae if done with a certain concept. These are gentle gift (in tune with nature and man, unlike the general hermetic), major magical focus (which really could fit any hermetic or non-hermetic style), mythic blood (latest of a pagan god's dynastic line as opposed to founder's line), and secondary insight (which is basically certain forms and techniques the tradition specializes in will be increased faster as a whole when studied). Flawless magic could work with a more narrow focus than the general virtue- say the benefit from the first level of mastery is always the same- thus a tradition that shaped spells on the fly can quick cast any formulaic spell it learns, another that specializes in overcoming other magic gets the penetration benefit, etc. The only virtue that's entirely inappropriate would be mercurian magic (which is more closely tied with hermetic magic).

2) Opening minor up to supernatural virtues. This should be a no brainer. The defining point of Ex Miscellaneae is it's embrace of non-hermetic magic. Supernatural virtues are the best representation of that. Given that Strong Faerie Blood makes one more inclined to Merinita if that's a defining point of one's magic, and that greater immunity and greater purifying touch have limited application, there are simply way more minor supernatural virtues that are good for helping to define an incorporated non-hermetic tradition. (And if you think that greater immunity and purifying touch are good for defining a tradition, there's no reason why the lesser versions wouldn't be as well).

3) The general minor virtues are really a judgment call by individual groups, but certain ones will probably be seen as tradition defining more than others. The bonuses to certain mental and physical activities like clear thinker and enduring constitution could be a result of mystical training. "We strengthen our minds against the deceptions of the world" or "We channel the energies of the land to lift some of the weight of exertion". So too great characteristic and improved characteristic, though where the points go would be based on the tradition. Piercing gaze could be mere stance or magical effect. And finally venus's blessing could be because the tradition promotes that kind of attraction magically or is favored by some external magical force a la Venus.

4) Dissallowing certain minor hermetic virtues- anything the group feels is tied strongly to being hermetic- Obvious call is method caster. A number may feel that Adept Lab Student is closely tied to the common understanding of hermetic magic. Also hermetic prestige. This depends on the particular troup, but general canon on this has been that non-hermetic ways does not garner hermetic prestige.

All of that said, nothing should necessarily allow the player purchasing these virtues normally. The purpose of the Order is to gain it's benefits, and there's no reason why an Ex-Miscelleneae shouldn't be able to do that, or to overcome the taint of being a hedge wizard to rise in prestige. It's just that those virtues don't define his separate tradition, and thus shouldn't be one of the freebies.

This is my view, at any rate.