I think this is unfair because npm has its own set of issues, most notably, if anyone were to sneak up a non obvious trojan horse into the dependency chain, it would take a few weeks to be detected and millions of servers would already be compromised. You can do this with deno too but the norm is to use pinned version and a deps.ts, it takes a bit more than just an innocent npm install to break things.
The real security for scripts is in the sandboxing, permissioning model and providing self-contained scripts that you can read and analyze in one go. So far, node doesn't offer that experience yet. Deno is the leader of innovation in that specific area. It was a bold move and that it is moving back to node compatibility has a lot more to do with network effect and first mover advantage than an inherently bad design.
Bun is likely to have made the correct move by focusing on performance and node compatibility from a business/adoption standpoints (and we will add bun to our supported env as a consequence), but from a security perspective, deno is still the cutting-edge.