I completely agree with your perspective. The essence of a Bethesda game, and many other sandbox-style games, is the freedom to tailor the experience to one’s own preferences. Removing a mod that is essentially harmless takes away from that freedom and raises questions about the influence of ideological stances in the moderation process.
As you suggested, locking the comments could serve as a reasonable compromise. It would allow those who wish to use the mod to do so, while mitigating the potential for inflammatory discussions. This way, the community retains its diversity of choice without being subjected to a single viewpoint.