If there is a separation ‘let her remain unmarried’; the marriage bond is still there. This may be cover the situation that has arisen because some people have left their pagan husbands even before the apostle was asked this question, and before he gave his reply.
That is an extreme position. The pastoral effort must always be to keep people together, unless there is adultery, unless there is abandonment, or unless there is cruelty or intolerable violence, in which case it is criminal and it is not safe. But in all other circumstances our first aim is to try – they are professing Christians, after all – to try to reach the point of repentance and change, of reconciliation and harmony, if it can possibly be done. That is always the first aim of the church of Jesus Christ.