Yes, I would say you do. When I did all the Munros and Tops I was very careful to do every summit that ever had or ever would be one of either - just in case. And doing the Tops is important, first because you see the whole mountain properly and second because some of them (e.g. the Northern Pinnacles on Liathach) are very fine places in their own right.Surely you have to do all the "deleted" ones as well in any case if you're a true compleatist.
People who don't go hill walking or climbing often have completely the wrong idea about Munro-bashing. Yes, there is a list, but it's as much a historical document as a tick-list; and the advantage of any arbitrary list is that it takes you to places you wouldn't otherwise have thought of going to - "It gives a purpose to wandering feet", as Hamish Brown put it http://www.amazon.co.uk/Hamishs-Mountain-Non-Fiction-Hamish-Brown/dp/1905207336
The scoffers have this notion of bands of obsessives, trudging up well-worn paths, never raising their noses out of the sacred text and never doing a hill that wasn't on it. That hasn't been my experience and, believe me, I've met lots of them. All the Munro-bashers that I have come across go to plenty of places that aren't Munros and do many things other than hillwalking. If you want tedious obsessives, try TT cyclists or, worst of all, triathletes.