That crucial flaw is the fundamental structure of our legal system. It's why case law is a valued and necessary part of our legal doctrine. Humans are bad at predicting the future, and attempts to write prescient laws often end with significant loopholes that must be corrected after the fact.

That this system fails to work when it's axioms are ignored (i.e. in the stated case of a coup) cannot be construed as a failure of common law or an indictment on its 950+ years of success. Such act would be a failure of the Executive solely.

The founder's stated intent for resolving such a situation is why we have the 2nd amendment.

It doesn't matter. In the case where the president is using military force against political opponents it doesn't matter what the law says anyway.

It aims to be "rules for thee but not for me", and the court's choice of who they hold to the rules. It's a more realistic and relevant flaw.

There's one crucial flaw: you could neutralize the president in such a patently extreme situation and be acquitted by the jury

These days I wouldn't expect anyone who makes an attempt to "neutralize the president" to live long enough to see the inside of a courtroom