Loyalty is a virtue, is indeed the primary virtue in many societies - but it is a minor virtue for a Christian. Therefore, when a Christian finds that loyalty is becoming his primary motivation - he can be sure that he is being corrupted away from Christ.
The original, traditional and ancient, loyalty was properly to an individual person (the the 'liege lord'); and the idea of loyalty to an abstraction - such as an organisation, the personnel of which are completely replaceable - is a development, and a weakening of the original.
Too many Christians have been more loyal to their church, abstractly conceived, than to their faith - but this loyalty is being tested more and more strongly with every passing year and the corruption of large and powerful Western Christian churches is being revealed as more and more extreme.
This is a test of Christian faith, and a necessary test. We ought not to 'complain' about it - because it reveals our own lack of faith.
It used to be possible (in many times and places) to be a passive Christian, and treat a church as if it was itself the abstract and incorruptible perfection of faith. The church was regarded as intrinsically and necessarily and essentially pure, regardless of the people in it.
(Because it is assumed that the one absolutely reliable area of direct divine intervention in this mortal world, is for God to ensure that the leaders of this church are always and under every circumstance essentially pure and true; never corrupt and false...)
An organisation was thereby regarded as better than actual people. This is a common modern belief, associated - in the twentieth century - with bureaucratic totalitarianism; on the tacitly-assumed basis that individuals are always corrupt; but when Committees follow Procedures, then Good can be made routine, reliable and objective.
The falseness of this hope should have been obvious - but is not obvious, it is very far from obvious to many or most people - including most Christians; and therefore the test continues, and continues to become more extreme.
It seems to me that, so pervasive is this test, that it is a high priority for our God to confront us each with the choice; to put us into a position where faith and loyalty are in stark conflict so that we are compelled to choose.
This seems to be a lesson that we must learn, hence cannot avoid (although we can, of course, continue to deny it - and to insist that there cannot ever be a real conflict between loyalty and faith - but that is also to choose).
Note added: If corruption has not yet come to the leadership of your church, then it must be that that church is distinct from the current mainstream. In future, purity and strength of faith will only be maintained insofar as a church is pretty-much cut-off from communications with the social systems of politics, the economy, education, employment law etc - because the bureaucratic requirements for participation in the mainstream are corrupting - ever more comprehensively and intrusively, and by design. Benefits are available only with strings attached; these strings bind to the mainstream; and the mainstream is ever-more-explicitly anti-Christian, pro-evil.