I haven't read all of the threads and haven't checked in on this case in a while, but do we know for a fact that she was shot? Has that been substantiated by LE? (Sorry that I'm not up to date.)
And if she was, couldn't she have been hit in the head with the hammer or pry-bar and then shot while she was unconscious on the floor as the assailant panicked about how to get out of the situation?
The short answer to your question is, "Yes, MB was killed by gunshot."
FBI UCR records exist showing that to be the case, and were discovered and brought to the forum when it reopened with Thread 45. We first heard this in Thread 45 Post 104. In the files referencing MB case's cause of death, it says:
Weapon
Handgun - pistol, revolver, etc
The records are online but hard to access, because it requires a search with just the right parameters in a massive database, that is part of a website. Two websites, in fact. So there's no way to link directly to the page, but when told about it, many of us here looked it up for ourselves. I did it multiple times, both places, but have no desire to do it again because it's so frustrating to do. If you want to delve into it further, you only have to read the posts since then, as there are MANY MANY explanations and discussions of those records since then.
Some more things to know:
1 LE has NEVER answered the question of MB's cause of death. In PCs they danced around the question, and basically said they will tell us later, and we're 7 years later and still not a word.
2 In a SW on Day 1, LE said that Missy had “deceased from a head wound”. They also said that "an unknown male used an unknown instrument to cause the death..." Nothing about puncture wounds and nothing about the chest (wording that came only in a single later SW). After that, LE stopped describing her injuries at all.
3 In a SW from Day 2, LE said this (which they have never explained further), which was what led us to the idea early on that she was not killed by gun: "
Terri Bevers’ had multiple puncture wounds found on her head and chest are consistent with the tools the suspect was carrying throughout the building."
4 In retrospect, that wording in that SW is incredibly unclear, almost weird. It tells us of wounds, but not whether they caused death. It speaks of "tools" the suspect was carrying, but doesn't say they are seen in the video.
5 What tools are actually seen - flashlight, prybar? But then where does that take us? A blow on or upside the head by a flashlight or prybar wouldn't cause a puncture, as puncture wounds are those that would have made a hole in the skin. And there were "puncture wounds" made in both head and chest.
6 From day one, LE brought ATF to the case, and there were early whispers around the case about dogs on the scene to sniff out things and about gun investigations (and about FOIA requests to reveal gun-related things, that were turned down on legal grounds rather than being told no such things exist, keeping things private). When we thought it was a stabbing death, those didn't fit at all, and caused much debate in this forum. Now, of course, it all fits after all.
7 We were also told by VI that the damage was minimal enough that the family almost had an open casket funeral, and kept it closed for emotional reasons but not because there was too much damage to MB. That perhaps hints of damage only by bullets that left a smaller footprint in the head and chest.
The idea that MB was injured by multiple things, and killed by gunshot, as you suggest, is certainly possible.
But some (myself included) have concluded that LE was being intentionally misleading in the SW, without actually lying, for the purpose of keeping COD info behind closed doors and away from the public. For us, LP was carrying a gun (but not seen) and killed MB with it, and then ran away (in panic and fear, I'm wagering).
In the SW wording, it doesn't say how many wounds there are, other than "multiple," and it offers 2 places that were punctured (head, chest), so it's possible the entire attack consisted of her being shot in the head and the chest, 2 shots total, and that was it. It would be informative to know more of what all happened if we had the coroner's report, but we don't.