When you go in to change her... do you talk to her and engage with her and what not? If so, then you are waking her up.
Try... when you go in there to change her... do it as quietly as possible, do not talk to her, be as swift & stealth about it as you can. And change her right there in the crib. Don't lift her out or take her to a changing table etc.
Then leave.
Keep the room dark.
With my kids when they were babies, that is what I did. And they'd continue to sleep/nap.
Even if/when pooping at night, just use a little tiny flashlight, to aid you while you change the diaper. That is what I did.
She can't help it, she is a baby. Pooping when sleeping startles them.
Or, put her to nap, after she has pooped. If she is 'regular' about when she poops.