I have an E92 and an E53 X5. I was one of the first one to get the M3 in Australia and the E90 was not available at the time. In my opinion M3 is a special vehicle and buying it in E90 would have been something very hard to live with for me given they look same as the regular sedan except for the front. Also no CF roof in the E90 and a lot of the standard items on the E92 have to be optioned in the E90.
I have a 15-month old daughter and I drop her off Day Care everyday and there is no issue getting in and out of the back seat. Although E90 is more practical if you're buying an M3 you should go for something that stands out from the rest of the 3-series range when you're spending that kind of money.
When we go out as a family we still use the E92 even for long trip and there is no problem. One rule in our household is no eating in any cars - drinks are fine. I think it is a good habbit not give the kids to eat in the car.
I've had the car for nearly 2 1/2 years and it's still in prestine condition. So it depends how you look after the car. There is no reason not to use an expensive car b'cos you have kids. Kids will be kids but if you instill good qualities in them when they are young later on there will be no problems. (God, this sounds like a parenting lesson
). This is my humble opionion.