Yes, in order for a player to CD, they need to miss two phases (ie, not open the game) where they have orders. Two NMRs will increase their NMR counter, but won't put them into Civil Disorder.
(Note: the NMR counter is currently broken. Stay tuned for an update on that sometime this week. Don't worry, they've been correctly counted so far, just not displayed).
The intention of this rule is to put players who are no longer playing in to civil disorder. NMR count is included in the upcoming reliability rating, so players who are NMRing but not CDing will still be punished.
You're right that it'd be a small improvement to change it to two NMRs rather than two missed phases. But with a todo list as long as ours is, I don't think we'll be making this change soon.
I think it's a low priority because players won't avoid reliability punishment by avoiding CDs but still NMRing. And, as noted above, players can enter all holds anyway, so if someone really wants to troll to throw a game while protecting their rating, they still can.
However, we're planning to have a pretty active year of site improvements - including reliability ratings and the ability to add games to a watch list (so you can follow games that you're not in). And many other small improvements and fixes.
~webdip programming team