I'm sorry, I'm still not sure what you're asking. You want to know why Holy Magic is good for a magus character, as opposed to just taking a set of Supernatural Abilities? I'll try to address that.
First and foremost, it's a setting/character thing. The character can do magic, but backed by the authority of the Divine. Magic can be a questionable thing philosophically, but this character is sure (surer than most) that he and Heaven are on the same side.
Secondly, the Dominion covers most of Mythic Europe, at least the parts where people live. Holy Magic never receives a penalty because of the aura, and receives an aura bonus in every realm but the Infernal. If we're comparing it to Faerie Magic, this is much, much more powerful. The magus can actually live in a Divine aura, which penalizes all other types of supernatural beings.
Casting spells with long-term Fatigue instead of vis may not seem like much of a benefit, but consider a city or covenant under seige. The holy magus with a CrCo specialty can heal a heavy wound every other day, with no other cost but a place to sleep and simple food to eat. The character could even create the food himself. Momentary rituals are really where this shines.
The special Ranges, Durations, and Targets are much more powerful than Hermetic ones of the same level. Compare Sun and Sabbath, for example, or Moon and Fast. There's also twice as many as Faerie Magic. I think the differences between the Minor Virtue and the Major Virtue are quite noticeable here.
The ability to use the guidelines for Methods and Powers with their magic is a substantial benefit, but it's an added one designed to reward characters with True Faith who join a societas. Such a character can learn the favored Abilities of the tradition simply by finding a willing teacher, and with them can break Hermetic limits in a fairly broad way. This is sort of like Faerie Magic's role as an Outer Mystery: it allows you access to more powerful magic, but it isn't useless without it.