I don't think how easily someone can duplicate your site is a reason for concern. If they can duplicate it in a weekend, you probably don't have much of IP value. If the proprietary system makes it easier to develop, then it may be of some value. If it makes it harder to develop, then you have shot yourself in the foot twice.

Someone trying to reverse engineer your site probably wouldn't use anything of yours. They would start fresh with their own set of tools.

I am pretty much biased towards open source, because it's cheaper, evolves faster, and you can mix and match.