Intertwined within this story are many rather simple points ...having endured how long-winded I am, please bear with me for a few more crucial points:

1) God loves us ...and that includes freedom of choice.

2) We have freedom of choice ...and that means we can choose against God, against His love.

3) God is righteous ...He will not allow your freedom of choice to forever infringe upon my freedom of choice, especially when it is detrimental to me, therefore it may seem necessary to separate those holding views in conflict. (That does not mean that when my spouse and I have a conflict, we must be separated, nor do the children board up their bedrooms and forbid me to enter.  Most conflicts can be reconciled, and we look to God to guide us through the process.  Yet, when we have huge ideological differences, it may not only affect how we interact with others, but also how we respond to God.  Though we may not agree, this separation is through our own doing, by our freedom of choice.  It is important that we understand what we are choosing though. And reconciling should not be a process of making us feel comfortable with turning from God's ways ...but by repenting and turning back to Him.)