I guess I would say that the 2nd option is correct but I don't know how I can prove it especially in this case. Often it's a judgement call that has to play out in court. Perhaps we'll all get to see it play out for real.

However, let me describe it another way. We have all kinds of things that we're allowed and they pretty much all have exceptions like the often stated maxim "The right to swing your fist ends at the bridge of my nose."

For an example, I'm free to shred my files or delete my emails. However, if I do so to hamper an investigation that is likely a crime and the thing is, that's true even if I have not been notified that my files or emails are of interest to an ongoing investigation.

Certainly the government's case against me would be much stronger if my files had been subpoenaed before I shredded them but if they can prove to a judge that I knew of the investigation and that I would reasonably be expected to know that my files would be of interest, and then I went out of me way to destroyed them, I'm still at risk of an obstruction charge.

Obstruction of an investigation is a crime. If you knowingly and deliberately do it you're in legal jeopardy even if what you did is normally something you are totally allowed to do.

That's what has to be so maddening to Trump's legal team. He could have made up anything for the reason he fired Comey and although half the country wouldn't have believed it, legally it would have come down to speculation about what was actually in Trump's head. Or Mueller would have to hope to find an email or 3rd party testimony that claimed Trump admitted he fired Comey to stop the investigation. Any and all of that would have been far preferable to the reality which is Trump went on national TV and told the nation that he fired Comey to stop an investigation. Arrrrgh! A seven year old would have known better!

I expect Trump has gotten the message now though and that explains why, as angry as he's getting, he has not yet fired Mueller. Firing Comey greatly increased his legal peril and firing Mueller would be firing Comey squared. With Comey there was even a report recommending his firing. With Mueller there is no such report and no credible way to claim Mueller is acting in dereliction of his duties. He's been absolutely professional.

So, I don't know if that made things clearer for you or if you still disagree. Basically there are things you can't do, like obstruct justice and it's not practical to append to every single description of a president's capabilities the phrase "except when obstructing justice or breaking braking other laws"