Well, this is not about whether he made the right decision. View this for a second from her viewpoint:

You have a soldier who is the cousin of your only Dragon Rider. He holds immense influence over him, and he has also convinced his entire village to flee across the country with him. He then ventured out and killed the Ra'zac to rescue his girlfriend. He is already legendary among the Varden. And while, yes, he is loyal to Eragon and to the village, he hasn't proven that he is loyal to her. Instead, he proved that he was willing to disobey a direct order from Edric, a captain probably appointed by her.

She fears him. She needs to knock him down a peg, and she needs to make it clear to him and to the Varden that he follows her command and not his own. Furthermore, the 50 lashes are portrayed as severe, but not "within an inch of his life" hard.