It doesn't take bad intentions to end up destroying an open ecosystem, just a lack of effort to create standard solutions while being the majority market share gorilla.
Microsoft employees likely thought they were doing good by adding non-standard features to IE as well given that "standards couldn't keep up" for them either.
NaCl solved real problems people had. NaCl allowed secure native code inside Chrome extensions and webapps, before Asm.js and before WebAssembly. It helped with removing insecure NPAPI usages (in the past, a Chrome extension could contain an NPAPI plugin![1])
Nowadays, NaCl is a lot less necessary. Many apps can run just fine in Asm.js and WebAssembly. This is definitely due to cross collaboration from the browser vendors, improving JavaScript performance and solidifying the idea of a cross-platform, safe, portable binary format that could be implemented by all browser vendors. That seems like a fantastic outcome to me, as an end user.
Other browsers could've implemented NaCl if they pleased. I recall Mozilla pushing for pure JS and later asm.js instead. In the end, the solution we really ended up with is a lot like a mix of NaCl and Asm.js. You could argue we would've gotten here without NaCl, but I think the end user is certainly better off without things like NPAPI plugins.