Yes, there are those cases - the Biblical reasons to seperate oneself - crossed my mind as I typed the first post here as well, as I had just yesterday posted to that 'Church at Ephesus' thread.
These are the verses from that thread -
Rom 16:17, 18 Now I beseech you, brethren, mark them which cause divisions and offences contrary to the doctrine which ye have learned; and avoid them.
For they that are such serve not our Lord Jesus Christ, but their own belly; and by good words and fair speeches deceive the hearts of the simple.
2Thess 3:6 Now we command you, brethren, in the name of our Lord Jesus Christ, that ye withdraw yourselves from every brother that walketh disorderly, and not after the tradition which he received of us.
2Thess 3:14-15 And if any man obey not our word by this epistle, note that man, and have no company with him, that he may be ashamed. Yet count him not as an enemy, but admonish him as a brother.
1Co 5:11 But now I have written unto you not to keep company, if any man that is called a brother be a fornicator, or covetous, or an idolater, or a railer, or a drunkard, or an extortioner; with such an one no not to eat.
2Jn 1:10, 11 If there come any unto you, and bring not this doctrine, receive him not into your house, neither bid him God speed: for he that biddeth him God speed is partaker of his evil deeds.
This is a sad topic - needing much prayer behind it.