They can’t indict Trump. You are missing the obvious: Trump can fire any Prosecutor who tries to indict him. The DOJ already has issued a policy that says a sitting President cannot be indicted. You may think the reasoning is flawed and does not apply to Trump, but how exactly can the policy be overturned? Will Trump’s appointees issue a new policy?
You’re also missing another obvious point. If an indictment is issued and Trump refuses to honor it, the US Supreme Court will almost certainly rule in his favor. No one will want a showdown over this issue.
The branches are co-equal. The Judicial branch has no power to impose any process on the President. The Constitution allows only one remedy: impeachment and conviction.