I'm glad you posted here because when I posted this about a year ago no one seemed to know anything - but I did a ton of research and now I can help you!
So, my situation was like yours - went for my 6 week checkup and my Dr was not satisfied with the progression of healing. As for the nitty gritty, I had a 3rd degree tear and a blood blister, it required um, extensive, repair. So at the 6 week appt Dr prescribed Premarin (conjugated estrogen) w/ .625 mg per gram. I used 1 gram, I think, intravaginally for a week. After that week I was having some extreme breast pain (which I later found out was thrush, ah, the days of being naive) and called in because I thought it was a side effect of the estrogen, the nurse told me it was fine to quit using it. When I went back at 8 weeks the Dr was happy with how I was doing and told me to use it as needed. Haven't used it since. Good thing I have good insurance.
As for the hormones, based on the research I did I was not too concerned about supply. And after using it my supply was not noticibly effected. Although they are synthenic hormones they are similar to what your body would naturally produce. I can't imagine I wasn't producing at least that much estrogen when I started my periods again at 3 months pp. Yes, some of those hormones can pass to your babies, in my opinon that is negligble.
The unfortunate thing is that I could not find another Dr, a nurse, a pharmacist, no one, who knew anything about this. Because this product is usually prescribed for perimenepausal and menepausal women all the information deals with that client base.
As for other ideas for healing - keep using your peri bottle, sitz baths, maybe some ky lube. The idea is to keep the area moist so it can heal. Wear loose cotton underwear.
And now for an unsolicited point - sounds like your doctor may have made an error in your surgery. I don't know the details of how or why healing correctly might not occur. It seems to me that it is one thing to have not progressed to a satisfactory level, yet another to have to go back and fix something. Perhaps a second opinion is in order? Just a thought.
I will check back if you have questions or you can PM me.
And I can't believe I forgot to say - congrats on the twins!