The problem with your point of view is you are not making the distinction in criminal procedure, as the Constitution clearly does, between Officers of the U.S. and underlings.
I don't see the problem or issue as you see it. We agree that the constitution gives congress the sole power of imeachment and removal from office, but I think that's the only thing we agree on.
Judgment in Cases of Impeachment shall not extend further than to removal from Office, and disqualification to hold and enjoy any Office of honor, Trust or Profit under the United States: but the Party convicted shall nevertheless be liable and subject to Indictment, Trial, Judgment and Punishment, according to Law.
I don't read that as indictment depending on impeachment; only that impeachment does not substitute for or preclude indictment.