The original article is better than this hot take on it, although it seems to make a lot of assumptions as well:

While the underground tunnel uncovered by Israeli forces after the raid does point to a possible militant presence underneath the hospital at some point, it does not prove that a command node was operating there during the war.

The article admits there were likely militants under the hospital, which I believe would make it a legal target. I'm not sure why it would have to be a, "command node," which is what this article seems to focus on.

The Post mapped the path of the tunnel by geolocating the excavation sites within al-Shifa and analyzing the videos frame-by-frame to determine the network’s directionality and length. The Post then superimposed the tunnel routes on the original map released by the IDF on Oct. 27 that it said showed the full extent of Hamas’s command and control infrastructure.

Now this is the most interesting claim the article makes, that the footage IDF released does not prove that the tunnel networks they showed footage of connects to Al-Shifa. It still might, but the video does not conclusively show that. US intelligence sources agree with IDF's assessment, but they aren't sharing their sources so I suppose the credibility of this depends on one's perceived credibility of US and Israeli intelligence agencies.

IDF released video footage showing spokesman Jonathan Conricus walking through the radiology unit. Behind an MRI machine, he points out what he calls a “grab bag” containing an AK-style rifle and an ammunition magazine.
Photos released by the military later that day purported to show the full haul of weapons recovered at the hospital — about 12 AK-style rifles, in addition to magazines of ammunition and several grenades and bulletproof vests.
The Post was unable to independently verify to whom the weapons belonged or how they came to be inside the radiology unit.

So they have evidence they just don't have the full backstory of how the guns got there. I'm not sure how they would expect the IDF to establish this or why this diminishes the evidence.

IDF published an additional piece of evidence: security camera footage showing armed militants leading two hostages through the hospital on Oct. 7 — among some 240 captured during the assault on southern Israel. One appeared to be wounded and is on a gurney. It was not clear if the hostages were taken to the hospital for medical treatment or other purposes.
Hostage-taking is a crime under international law. But “misuse of the hospital five weeks before the IDF operation does not bear on the legality of the IDF operation,” Haque said.

Oh it doesn't count because they brought hostages there a little while before the bombing? Please.

After arresting the hospital’s director, Ahmed al-Kahlot, Israel released an interrogation video Tuesday in which Kahlot admitted to being a member of Hamas and said the hospital was under the control of the Izzedine al-Qassam Brigades, the group’s armed wing. In response, Gaza’s Health Ministry said the statement was made “under the force of oppression, torture and intimidation” to “justify [Israel’s] successive crimes, especially against the health system.”

This seems pretty damning, despite Hamas' denial. I have seen no evidence that this confession was obtained by illegal means.

All of this together certainly makes it seem like the hospital was used by militants, despite the article's skepticism. They just gloss over this and focus on anti-IDF conjecture.