I feel like I didn't read the same comic as some of the people commenting here??
The reason her work is not accepted is outlined in the very first page. Kei is extremely uncharismatic and her work has huge ethical concerns. The latter part is what this entire comic is about. Granted her presentation didn't necessarily involve the romance code, but sentient customizable AI is pretty inherently rough territory.
She gives a breakup speech to a mere robot because she is human and did see Marie as a lover on some level. She questions herself after the fact why she didn't just cut that step out. It's not like the author just forgot she could do that.
I also really don't feel like the comic "suddenly got dark". The setup should be very unnerving if you think about it for even a second. The twist seemed pretty inevitable and like an appropriate exploration of the dynamic to me.
