Doing Right the Wrong Way

I Samuel 13-14

Saul, indeed an intriguing fellow. He decided that he was tired of waiting for Samuel, the priest, so he offered the burnt offering himself. His impatience assured him that he would not be king forever.
13:13
And Samuel said to Saul, Thou hast done foolishly: thou hast not kept the commandment of the LORD thy God, which he commanded thee: for now would the LORD have established thy kingdom upon Israel for ever.

I must admit, I am a little confused about the story with Jonathan. He initiates a great battle against the Philistines, and Israel has a great victory. Saul tells the people not to eat until the evening. Jonathan, not hearing his father's command, eats honey. The people tell him of his mistake and then he tells the Israelittes to enjoy in the spoil even meaning they eat the blood the of the animals they spoil---a known wrong for the Israellites. Saul tells Jonathan he must die for his disobedience, but the people saved Jonathan and his life is spared.
Jonathan didn't directly disobey, but he did later when he encouraged others to do wrong. I've never heard stories about Jonathan in a bad light, but I would think this is not a good example of Jonathan here. He may have had his life spared, but this may be the reason why he is not chosen to be king later. Usually the son takes the father's place, even when the father is wicked, but this one is completely taken from their family lineage.

Both of these accounts remind me that the end does not justify the means. I must not take God's commands lightly and do them in my own manner. What are my motives? Do I go about doing right in the wrong way? Do I speed to get to church on time? Am I dishonest in giving taxes, so I can give more to the church? Do I help others, but disregard to help my own family first? Help me Lord to do right, rightly.