It is probably a sensible bias; with temporarily limited resources it makes more sense to concentrate them on the most-used lines. It's not just Northern; Marston Vale services remain bustituted.
I would say that the lesser need for rural areas is already reflected in the sparser standard timetable.
That sparser timetable should be reduced in proportion with more frequent services elsewhere. There is no justification for a more swingeing range of cuts to these services - if anything the sparser underlying service should result in more caution when it comes to cutting things.