I think the biggest risk of antibiotics is that the baby might not get the healthy dose of "good" bacteria while in the birth canal. This could lead to the baby not having the proper bacterial balance in his/her gut. An extreme dosage of antibiotics (like in the case where you get a dose every 4 hours, and your labor is 32 hours long), could cause a yeast overgrowth and lead to thrush. Not fun. But I haven't read anything specific to vernix.
However, you need to balance those risks with the risk of the baby contracting GBS. Without meds, I think it is a 1 in 200 chance (in the US---it's 1 in 500 in other countries, like the UK). With meds, I think it is like a 1 in 2000-4000 chance. I can't remember the exact statistics, but you would have to just look it up. I would recommend doing your own research to decide whether you want the antibiotics.
I am considered a GBS carrier because I have tested positive on a couple different occasions. I had the antibiotics with my first. It was not big deal. I labored at home for a while to avoid an increased risk of hospital interventions and receiving an extreme number of dosages of penicillin. I had thought about not getting the meds for my second birth, but after researching and weighing different scenarios, I have decided to get them, again. What it basically came down to for me was that I would rather receive a standard dose of a first or second generation antibiotic than have my baby contract GBS and have him/her get pumped FULL of much more powerful meds.
So just keep reading up on the subject and do whatever you feel more comfortable with. There are some home-remedy-type treatments (a garlic regimen, for example) that you could look into. There are no studies to back them up, however. In my opinion, that doesn't mean they don't work---it just means that no one has taken the time or spent the money to study them. But for me, without that clinical support to show they DO work, I plan on using them as a supplement to the antibiotics.
Also, keep in mind that if you are having a hospital birth, refusing the antibiotics will affect your length of stay and whether they run additional blood tests on your baby. They will typically keep you longer if you don't receive the meds, so that they can monitor the baby for signs of GBS disease. That could just be an added inconvenience for you and not something that is a deal breaker, but it is another factor that you might want to consider in making your decision.