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I think you could define your own mutt package that doesn't have the optional stuff, although it may be a lot of work.

I don't know much about the nix language, but it looks to me like the gpgme support is optional:

The thing is easy to fix. The problem is that (i) most packages are far from minimal (ii) you loose pre-built binaries.

True enough. I wonder how much of the problem comes from trying to be compatible with software packages designed for other systems.