I'm going admit this then move on; this is not a new idea. Nor is OoH: CSI, (HoH:TL already did that).
The 'Mysteries' are in fact Mystery Cults, (not the House Mystery Cults, though I'd like to hear your thoughts about that).
Imagine somehow, an unitiated Bonisagus researcher comes across some 'mystery spell' lab texts and, noticing the differences between standard magic theory and them begins to research integration, rather than self-initiation. If the Bonisagus succeeds, then he/she gets the appropriate Virtue. Fairly simple and sound. If the cult hears it tries to prevent the research.
Now imagine it doesn't end there. Maybe the Bonisagus recognises someone had already partially worked it into hermetic theory and the current research only recreates it. Maybe he/she is just stubborn. Regardless, the Bonisagus continues until he/she has fully integrated it into hermetic theory, to the point that the 'virtue' is part of the package, like certiman. Naturally that is when our industrious little researcher tries to distribute the breakthrough.
And that is when, assuming they have been ignorant of the research so far, the cult finds out.
So how do you think they'll react? I can see it varying between the varies 'schools*' and cults. (Bit of a difference between incorporating Names of Power compared to Hermetic Architecture). Likewise, what methods do you think the mystery cult would try to prevent the research? Wizard Wars, scrying, accusation of crimes (since Mystery cults think they derive power from being secret they might try calling the research 'deprivation of magical power' because the secret is out)...how far do you think some groups will go?
*meaning the types of mystery, see TMR.