Yes, you can replace Bonus Disciplines with any other discipline.
As you note, the Psionic Disciplines feature says:
In addition, whenever you gain a level in this class, you can replace one discipline you know with a different one of your choice.
When you gain a level in the mystic class, you can replace any discipline you know with any other discipline. And as you've noted, you learn the Bonus Disciplines gained from your Mystic Order, after which you know them. Thus, those disciplines can be replaced upon level up, just like any other.
Rules designer Jeremy Crawford confirmed this ruling (and its significance) in a concise pair of tweets in March 2017:
When replacing disciplines known upon level-up, can you switch disciplines granted by an order with ones of another order?
So in the long run, the fact that the extra disciplines must be from your order is more of a flavor thing, right?
Ultimately, the requirement that the bonus disciplines must be initially chosen from those listed for your Order is not meant as a hard limit that restricts them forever - simply as a reason to pick additional disciplines that fit the flavor of your mystic order.