> What happens to someone who is convicted in a case where the law is both clear and clearly wrong?

Same thing that happens most of the time now. They serve their sentence unjustly. If it’s a serious issue, the Congress can act.

> You need something else

You don’t. Most societies don’t. Pardon power is an anachronism nobody would argue for if it weren’t already here.

> sounds like the abolition of prosecutorial discretion sounds like the abolition of prosecutorial discretion

What? No. This is a unitary-executive thing. Prosecutorial discretion is unrelated.

> second is that you're passing the political speech version of the interstate commerce clause

Lots of thought has gone into this. One can write it competently. At the very least, the First Amendment would still stand.

> executive is currently the only elected official with authority over executive agencies. Suppose the head of one of these independent agencies goes rogue

They’re not! SCOTUS just confirmed this for the Fed. We have a mishmash of authorities, with the Congress clearly wanting some agencies to retain some independence. Most statute creating independent agencies contemplates how members may be fired. If the Congress wants to create a judicial-type independent agency, I don’t see why it shouldn’t be able to properly—the executive already magics these up with administrative courts.