God, I'm so irked by this
PR.
Meredith is probably bitter about whatever's going on with her and Derek, so she takes it out on Amelia.
Meredith has never been unsupportive of any relationship before, but she's been so angry all the time this season, and it's because of what's going on between her and Derek I do believe. Normal Meredith would be supportive or carefree about what Owen and Amelia are doing. Of course Meredith isn't "normal" this season.
I'll choose to use how she finds out about them in Storm as my canon, because this is ridiculous.