It's not okay for a president to use "de facto confidentiality" to undermine or obstruct justice. Just have a private conversation with a subordinate regardless of the content and the prez is scott free? If that's the case, Nixon's conversations with all of his partners in crime should have been treated completely different.
Trump was attempting to recruit Comey, IMO, and had Comey cooperated, that would have made him a potential partner in crime. The type of loyalty Trump wanted wasn't appropriate. I know it's Trump's word against Comey's so naturally since Trump is Trump, then everything Trump says is automatically the gospel and Comey is the crook. Well at least to Trump supporters.
Trump was NOT "attempting to recruit Comey." :roll:
It is more likely than not the President was responding to the constant barrage of so-called "leaks" from "former and current members of the administration"...(in most if not all cases, of as yet to be proven true information BTW); and he was trying to find out who was reliable and who was not.
IMO that first conversation was his giving Comey an opportunity to let him know if he was going to be loyal and trustworthy to the new administration, or if he needed to be replaced.
Comey realized this, and instead of being honest and forthright, he gave an evasive answer. That was Mr. Trumps first warning.
NOTE: Asking a subordinate if they are loyal to the new leadership is NOT obstruction of justice. It is a reasonable concern in light of all the "disloyal" acts of those "former and current officials" who were actively trying to undermine the new Administration from day one.
The second was when the "Hope" conversation took place and Comey again gave an evasive answer instead of being honest and forthright.
In all probability, the final straw that broke the camels back was the report of the first conversation in (I believe) the New York Times which led to his discharge as a proven "leaker."
In the second place, in response to your first point. The President has the power, authority, and right to instruct any member of his government administration on how to use their time and resources while serving in his Administration.
He could have ordered Comey to stop investigating Flynn, and it would not be obstruction. He could pardon Flynn for any activities alleged to be a violation of Federal Law, and it would not be obstruction. Moreover, neither you, I, or Comey could do a thing about it...except vote in the next election.
As for de facto confidentiality? The issue is "leaking" information that was automatically considered confidential, as anyone who has served in government service or the military would know.