Yeah, he's putting many innocent people in jail, as a heuristic to reduce crime. One could argue it's a good thing, because crime levels have come down considerably and people can finally go out, enjoy a walk in the park etc. If 1000 innocent lives are saved from murder and 100 innocent lives are wasted in prison, a simple statistic like that would still support his policy.
But on the other hand, there is a difference between an ordinary ganster doing something bad to you and the state doing something bad to you. The state is a ganster too, but with much more power and special rights ordinary gansters don't have. So when innocent people go to jail, it's potentially a worrisome development, because it could lead to something worse. Bukele is often described as a dictator, but one that the people of El Salvador actually like and want. Some say good-willed dictators are better than democracies. But can we trust he'll remain (or even is) good? Trust in a person or institution is not in line with the philosophy of Bitcoin.
If most criminals are men, jailing all men would reduce crime by an order of magnitude or two, but as a man I wouldn't support such a policy.