No. Are they much trouble for you to deal with? They are weak sauce to me. I enjoy my encounters because I get to loot their armor(often bows and other weapons too) which can be improved to a pretty decent selling price by thowing some leather at it.
Actually, they will only fight you if you are in the Dark Brotherhood. The Morag Tong and the Brotherhood are enemies, after all. You will also find a Writ of Execution on them that state you are a part of an "unlawful" group of assassins.