The order is stated to require any mage who has general magic resistance to "join or die", does that include people with true faith who initiate into a holy tradition?
No, only people with Magical powers, who get their MR from something associated with the Magic (or possibly Faerie) Realm.
Not people with True Faith, or the pope or kings - all of which get a certain amount of Magic Resistance from the Divine. Or people who can grant MR with divine Methods and Powers.
Nor infernalists who have their own ways of getting MR.
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.
In general, the Order tries, and with good reason, to simply steer clear of agents of the Divine - and of the Infernal! No join or die for them.
However, it would not always be clear to a Hermetic magus whence the powers of some strange "hedge wizard" came. This is particularly true of traditions straddling two Realms, such as a Holy Sahir (or maybe some Folk Witches who "pass their gauntlet" by acquiring, and thereafter ever keeping, a minor Divine Relic). In these cases I'd expect Hermetic magi to investigate and eventually to come to some conclusion ... which might be wrong. And if the conclusion is that the powers involved are neither Divine nor Infernal, sure, it's join or die.