Let me first state that there is some incorrect information in your question. Joseph Smith never practiced or condoned Blood Atonement that was purely of Brigham Young's teachings. 
 
These two issues have different explanations so I will tackle them one at a time for simplicity.  
 
First is why do we now condemn polygamy? 
 
The simple answer is we do not condemn polygamy, but lets go more in depth to full answer this question.  
 
Polygamy is a biblical practice that us governed by the laws set up by God in the various times in history.  
 
God re-established laws for plural wives in the time of Moses (Exodus 21:10). We know this practice was allowed before Moses' time because Abraham, Isaac, and Israel (Jacob) all had wives and concubines and were righteous men of God.  
 
In the Doctrine and Covenants section 132 at the very end of the section, the laws regarding plural marriage are reestablished in this dispensation of time.  
 
Plural Marriage was practiced in the Church until 1890.  
 
The reason for this discontinuance (not renouncement) of plural marriage is because the US Government outlawed the practice of polygamy in 1862. This law was challenged as unconstitutional and was decided by the Supreme Court in Reynolds V. United States to be constitutional in 1878.  
 
So now the Saints could continue the practice of polygamy illegally or obey the law of the land (which we are commanded to in D&C 58:21). 
 
In 1890 President Wilford Woodruff declared the Church would stop the practice of polygamy in obedience with the Law of the Land. New Plural Marriages were still conducted in secret without the consent of the First Presidency until 1906 when this practice was stopped.  
 
 
At no time has the Church ever declared plural marriage evil only illegal.  
 
 
Blood Atonement was a teaching of Brigham Young and was never declared by Brigham or any church leadership as a revelation or a doctrine of the Church.  
 
The President of the Church is no less mortal or capable of making wrong decisions than any other man or woman. This is why in order for doctrine to be established it must be done with the unanimous decision of the First Presidency and the Quorum of the Twelve Apostles.  
 
Any other practices outside of declared doctrine is not official Church practice but the practice or belief of an individual or group of individuals in the LDS Church.  
 
I hope that this helps you understand these issue better!