Am I missing a few chapters? I don't see the big bad drama.
Yes, Aya's confused and shocked that her "Onii-san" is actually a girl, but that's pretty much it. She's not fallen into depression from it (yet?). Her world isn't falling apart (yet?). It's only just started to sink in, we don't even know her reaction to it, really. We've had two pages/*four panels* for her to react to it. This is being blown so out of proportion...
Arguing from the basis that Mitsuki has "deliberately misled another person in a way she knew, or should've known, would cause them great pain if they found out (as we saw happen in this very chapter)" is grossly misrepresenting what we've been shown (so far).
Asserting that it's "purely in order to preserve this pseudo-friendship pseudo-romance thing she had going on with her" is likewise ludicrous. The more likely explanation is how incredibly awkward fixing the situation would be for Mitsuki, who you might have noticed isn't the most outgoing and self-confident type.
There's a reason people stay in the closet for years or keep presenting as their assigned gender despite being trans, and it's not in order to deliberately mislead people in a way that would cause them "grievous harm". It's to avoid a presumably incredibly awkward situation that might amount to a social catastrophe.
(come on, we need only a couple more posts to hit 1800!)