That will be the typical dilemma of the Code: join or die versus "do not bring harm to your sodales", which the second part of "join or die" will sooner or later lead to if those Holy mages are well integrated in the society and/or the Church.
Now, keep in mind that according to the latest documents shared by Mr Chart, hermetic magic is supposed to be the most powerful magical tradition (including the magical resistance), so the "join or die" will be applied considering the threat or the benefits those mages will bring.
Considering that Holy mages will follow more closely than any other mage, tenants of the faith, they might not be such a threat - they are unlikely to go hunting magis (thou shall not kill). They might in fact be a good bridge between magi and the Church since they should be the living proof that magic is not inherently sinful - of course, it all depends on how closely they associated themselves with the local clergy.