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I don't think a factory reset will remove root but I could be wrong. I think the only ways to remove root is to unroot with z4 or whatever method you rooted with or do an sbf. If you have not installed the d2 bootstrapped you can just uproot and you'll be good to go. The best way to completely clean up your phone is to sbf, that will return it to "out if the box" new.
With limited pc access unrooting is the easier method. If you have used a bootstrapper than you can use a file manager from the market to remove the hijack folder in your system files. Google removing bootstrapper hijack file to get instructions on how to do it.