Where as the Holy Quran commands us to be obedient to the parents and to be serviceable to them, it also says:
“Your Lord knows best what is in your minds; if you are righteous, then surely, He is Most Forgiving to those who turn to Him again and again.” (17:26)
God knows it quite well as to what is there in your hearts; if you are righteous, then you should know that God forgives those who turn to Him. The Champions of the Holy Prophet, sallallaho alaihi wa sallam, were also confronted with hardships, and for religious reasons their relations with their parents were strained. But of course, it is for you to try all you can to be good to them and to look after them as best lies in your power; you should not lose any opportunity to serve them. Your good intentions will bring you good rewards. If you have to get yourselves separated from them, because of your religion, that, of course, is a thing, that you cannot help. But you should always keep in mind that you have to try to be good to them; your intentions must always be very good. You should supplicate to God for them.
It is not only you who have been made to confront with this kind of situation. Hazrat Ibrahim, peace be upon him, had also to pass through the same circumstances. However, you should know that your duty to God comes first. You should give preference to Him and try to do your duty to your parents as well; you should also be praying for them – and you should be very sincere in whatever you do. Your intentions must always be good.