Well, it also sounds like the OP wasn't told she would "have" to have a c/s but that she was at an increased risk for a c/s if she contracted the flu and then went into labor. Which, from the research and comments here, seems to be accurate.
It may also be that practice guidelines would prevent the midwives from attending a homebirth if mama had a condition like H1N1 or other complicating factor. If that is the case then the OP would be birthing in a hospital and that right there would increase her c/s risk.
As for being sick and going into labor... the body might actually kick into labor sooner in an attempt to "save" the baby or maximize resources for mama. I know a few women who have been very ill while giving birth... no fun.
OP- hope you stay healthy and have a fabulous homebirth!
