The reality is that God is merciful, but that isn’t quite the same as being tolerant. First, many people fail to understand the seriousness of sin and the great cost to God personally to forgive us our sins. When we see the combination of his holiness and justice we gain a greater understanding of his mercy. And that will go a long way to answering why he can’t tolerate sin and yet can be merciful at the same time.
There is a reason God can’t stand sin. You see, his core nature is holy and pure. There is no impurity of motive or action with him, for he is perfect and without sin. (See Deuteronomy 32:4; Isaiah 54:5; and Revelation 4:8.) So a holy God cannot be in relationship with sin in any manner. The Bible says of him, “Your eyes are too pure to look on evil; you cannot tolerate wrong” (Habakkuk 1:13 niv). He is so holy that he “cannot allow sin in any form” (Habakkuk 1:13). To do so would violate the very essence of who he is.