I gave birth at the birth center 2.5 years ago and are seeing them for this pregnancy as well.
I think that you should give birth wherever you feel most comfortable, but there are a couple of things to clear up:
1) The Birth Center wasn't "taken over by a hospital." This could refer to a couple of different things. First, they partnered with El Rio healthcare for funding because without it, they would have had to close their doors due to lack of funds. Second, they changed their group of "overseeing obstetricians" which is something that all midwife only birth centers must have to obtain malpractice insurance. Both of these things happened before my son was born and I never noticed a "clinical" approach my birth, so to speak. I couldn't have been happier, especially after seeing my sister's hospital birth a couple weeks ago...mine was nowhere near that clinical!!
2) One thing that skews the rate of birth that happen at the birth center vs. hospital is that some insurance providers will NOT let their patients deliver at the birth center due to their own hangups. There were a couple of people in my centering group who knew they would not deliver at the birth center because their insurance wouldn't let them. The midwives still attend to the labor at the hospital, however.
Another reason for the rate of hospital births is that some things automatically get you "risked-out" of delivering at the birth center. This is one thing that HAS been influenced by the overseeing OBs. The most common thing that would get you risked out is gestational diabetes. I think advanced maternal age is another.
I know this is long, and I'm not trying to sway you in one way or the other, I just wanted to answer some of your questions. Also, you can schedule an appt at the Birth Center and they would be happy to answer your questions. Lisa used to work at the Birth Center (I saw her once before I was pregnant and really liked her) so I don't think they would have any qualms about transferring your records to her.
Good luck deciding and I wish you the best of health and happiness on your pregnancy journey!