"The church was flexible on divorce because for 1000 years there was no sacrament of marriage, period."
Then to what is Augustine referring in "On the Goods of Marriage" and "Marriage and Concupiscence", Cyril in "Commentary on John", Clement in "Stromata",  or Tertullian in his letter "To My Wife" (to name only a few)?  It seems that even at an early date the Fathers recognized that marriage was a Sacrament.  You may argue that pastoral practice regarding separation was different from an historical perspective, but I think that the "period" at the end of your ultimate sentence is premature.