I'm going to take a guess and say the Emperor is some half-species or he has some weird magic or whatever that would normally make pregnancies impossible, Yalin getting knocked up is due to some random unforeseen thing as of yet unrevealed. That said the Emperor is connected to Yalin and is visiting her in her dreams, he can't make any outward moves to be openly affectionate to her or crazy bitches like that sister will come for her head, additionally if she's revealed to be pregnant she'll become a major target. The Physician knows what is going on with Yalin and probably has a hand involved, he's definitely a sort of shady individual and I doubt her going to him initially was purely random, that said I don't think he's evil so much as chaotic...
Personally I'll be waiting for the story to be more fleshed out and revealed before making a judgement.