From what I can tell, the problem they see is that stallman is proposing one standard word which applies and is correct for everyone rather than allowing everyone to create their own words and respecting their choices.
What Stallman didn't employ in his defence, and a fact also ignored by many proponents of 'they' who regularly cite its historical usage as proof of transphobia in anyone who refuses to engage in the practice the now, is that this historical usage was applied when the subject of the sentence was indefinite, whereas the modern call to use 'they' is in the case of a specific, known person. This usage does not have a long linguistic history, regardless of whether the existence of such would, in itself, form compelling grounds on which to continue its usage.
His claim about our ancestors is wrong. They made up new words all the time. Including alternatives to singular they.
Stallman uses the new pronouns for any subject not known to be male or female. Singular they was used the same way historically.