For a start, RR, I said it didn't matter- I specifically said it was just a film; I said the point was that my original criticism of ID4 had faded because I later realised that the original was no more credible.
Secondly, yes I do think the Humans fighting back is very important. It was an important part of the book and it should make it into the films. Simply having the aliens as totally indestructible- as opposed to merely ultimately unstoppable as they were in the book- actually reduces the impact. It's also rather juvenile to have an invulnerable, as opposed to a powerful, enemy; any five year old can imagine an invulnerable being; Wells' original aliens are a more intelligent design than that.
In fact, in the original, the aliens use of chemical and biological warfare- extreme concepts for the tme Wells was writing in- were in direct response to the humans fighting back, because they could be fought conventionally (although it was extremely difficult) and there were, after all, far more humans. This was a demonstration of how unready humans were for new types of warfare. The journalist (whose role turned into Tom Cruise's) who is the star of the book has the fortune of observing (or hearing from his brother) these things first hand, right over to the centerpiece fight of the martians against the Thunderchild, the famous picture of which adorns the front of the musical version.
Removing that is a change which I think weakens it.