Although I tend to lean more than a little towards the "put it back the way it came" crowd, I think I'd leave it off; I like vinyl tops but not every body style looks great with them and I prefer a contrasting color.
On the rust issue, my roof was mint (zero rust) under my vinyl top and although my car may be the exception, unless it's going to be a daily driver/winter beater then the decision whether or not to replace the top should have to do with aesthetics only: a properly done collector car not regularly left outside shouldn't have rust issues associated with a vinyl top.
Dave