Mono's problem is a patent issue. It isn't a software freedom issue. Mono is free software which is why it is included. Software with patent issues can be included in free distros assuming it is free (https://www.gnu.org/distros/free-system-distribution-guidelines.html)

Here is some more reading on the subject
1) https://www.fsf.org/news/dont-depend-on-mono
2) https://www.fsf.org/news/2009-07-mscp-mono

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