If one's conscience doesn't conform with the Church's teaching, it's incumbent upon a person to continue to struggle to reconcile one's views with the Church's teaching, never giving in to the tendency to simply hold "different or separate" criteria.   That's distance, un-communion, on an intellectual level. 

Seek guidance, read, pray, examine, ask for docility, humility, never stop seeking a "unity" with the teaching of the Church.   But the intellect needs to do its work, and not let one's pride tell oneself to develop one's own criteria.