I have several reasons. The first is, as we have seen in the SWs, it said Missy had multiple puncture wounds to the head and chest. Those wounds were consistent with tools that SP had been seen with and I believe left at the scene.
In one of the press conferences, it might have been the first one, A reporter asked a question (that I couldn't make out) and the reaction in response was "We did not say she was shot" - this may have been the first press conference so I would understand that. Sometime in May there was an article that appeared on the fox affiliate about the case and the headline had used the word "shot " (since changed) - the topic of the article wasn't about learning she was shot or anything like that. Now they have never stated that she "wasn't shot". They refuse to say the cause of death, that is, what was the fatal injury among all others and what weapon inflicted that injury. They have said that provides them with a "strategic advantage".
So, here is my line of thinking. If the wounds were consistent with the tools seen with SP (and I believe found at the scene) and one of those tools was the murder weapon what exactly would be a strategic advantage in not divulging that? If she had been shot, what again would be the strategic advantage in not divulging that? A tactical advantage, maybe. And just maybe.
There is that ATF K9. It was brought in for a reason. This was done the day after the autopsy, not the day of the murder, nor the day of the autopsy. Why specifically after the autopsy? If the autopsy concluded that the fatal injury (and all the other injuries) were caused by the tools found and no indication of the use of a firearm why do that? Naturally, why is MPD being tight-lipped about COD if there was no firearm involved.
Then there are the rumors. And I would expect that if they released the 911 tapes or the (redacted for names only) transcripts for those calls I believe we would hear or see the word "shot". Now, these people that found her wouldn't be able to make that kind of determination but to them that would be what they thought. Just how many people were at that scene that morning. You had the campers, EMT/Fire and police officers.
Missy had at least one friend that was a 911 dispatcher - no way of knowing if they were on duty at the time. She had several friends that were members of the fire department - at least 3 of whom (barring vacation or excused absence) would have been on duty at the time the fire department was dispatched to the scene. I find, with that many people that would know something about the scene that we don't have anything more reliable than the rumors that have surfaced.
** Graphic Warning **
So, my opinion is that the ME discovered something during the examination that indicated a high velocity impact - there would be indications of such throughout the brain, for example, away from any major wound sites. You wouldn't be able to create that effect with the tools SP had.
Killing Missy using the tools SP had would have been a bloody, messy affair. I expect that in most or almost all cases of hammer type murders that the initial blows are not fatal. So there is still blood under pressure as the wounds are inflicted and thus blood travelling relatively long distances. I can't imagine that we wouldn't have heard about a horrific crime scene area and blood everywhere. It would have been all over SP. Their gloves, equipment, and everywhere around. There would be blood drop trails, bloody foot prints and bloody glove smears on any door the killer touched on their way out. It would be no mystery exactly which way they left the church instead of the "we believe they left the way they came in". They would be finding blood outside. Unless SP removed all that gear close to or at the place Missy was killed and put in a bag. They would certainly need an extra pair of gloves, boots (or shoes).
Had she been instantly killed, for example brain stem injury that causes the involuntary muscle control and the effective automatic systems that keep us alive to cease functioning, then there would be no more blood pressure. Less blood at greater distances from the body. There would still be cast off if only a hammer were used.
To be fair, they haven't described the crime scene other than there was a lot of glass found around the body. As an aside I will note they did not say there was a lot of glass found under the body either. But, they apparently were able to finish up with the scene processing rather quickly.
For many of the reasons above I am of the opinion that the murder scene did not look like a text book hammer-as-murder-weapon murder scene. Similar, but not quite right.
This is only my theory so I could be wrong.