I'm not entirely thrilled with the cargo solutions here, but when I compare them to the options in other languages I think they're adequate.
If you're making a small change, you use a [patch] section in the Cargo.toml for your workspace if you're using one, or the Cargo.toml for your binary/.so/.a if you're not, and it will cause your entire dependency tree to use your forked library. You don't need to fork the entire ecosystem as you suggest.
The [patch] works at the "workspace" level (and you generally should stick your entire complex system under one workspace), so if you use that feature properly for your "complex system" (keeping everything under one workspace), it is a one line change to replace the dependency for your entire system. If you use multiple, well, one per workspace that produces a binary/.so/.a.
Also, for big enterprise projects, I would assume you would use a private registry in the first place, which is apparently well supported (though I haven't used it). That's how the enterprise places I work at have dealt with python dependencies for instance (I haven't used rust in a enterprise).
I can sort of understand people trying to maintain LTS linux distros complaining that for their purposes this is a bit of a pain compared to C style shared libraries (because they need to modify a lot of rust workspaces)... but to be honest I think that's a question of their package management tooling not rust's. Rust provided the tools they need to make their custom tooling work. As a user the number of times shared libraries have caused me pain makes me think that this static linking is the superior method of packaging.