What is it, exactly, that you think the word "sovereign" means? It simply refers to a Supreme ruler, or the font of authority. Why would God's sovereignty mean that He condones evil? Perhaps you are also confused about the meaning of the word "condone"?
For the world, sovereign is just an relatively impotent position, so we get confused about the definition of sovereignty related to God. IF GOD IS REALLY GOD, then nothing can happen without Him allowing it. If that is not true, He is not "The only True and Living GOD", but simply one god of many. If He can't bring to pass what He says will come to pass, then you can't bank on any of His promises; because He doesn't have the power to bring it to pass for you. But, God calls His shots. He always tells us in advance what He is going to do. If God could create everything from nothing, why on earth would you want to believe He can't stop something or make something happen, if He wants? Did He go from omnipotent to weak, in your sight? Think about what you are saying.
If I look at the world and decide what I see is what love or joy or peace is, and then I make that the definition I attribute to God, something isn't right in my thinking.
So how about this definition of Sovereign: "MY WORD will never return void; but, MY WORD shall accomplish that which I please, and MY WORD shall prosper in the thing whereto I sent MY WORD". (Isa 55:11) If Someone can say that and it comes to fruition, without exceptions, that Person is GOD.
Peter says this about scoffers: "For this they willingly are ignorant of, that BY THE WORD OF GOD the heavens were of old, and the earth standing out of the water and in the water; whereby the world that then was, being overflowed with water, perished; But the heavens and the earth, which are now, by the SAME WORD are kept in store, reserved unto fire against the day of judgment and perdition of ungodly men." (2 Pet 3:5-7) Jesus said it like this: "As it was in the days of Noah, so shall also the coming of the Son of Man be. For as in the days that were before the flood they were eating and drinking, marrying and giving in marriage, until the day that Noah entered into the ark and knew not until the flood came and took them all away; so shall also the coming of the Son of Man be." (Matt 24:37) We could talk about "If you love Me, you will obey My commands" and "If you keep My commands, you will remain in My love" and compare that with the human definition of love. And remember, "God is Love."
God's ways are always higher and often uncomprehendible by man--at least until we are looking in the rearview mirror and then we understand a bit better.