No, it's not going too far.
If you look at the argument ScotGov made at Stage 1 - vote yes, your concerns can be addressed by amendments at Stage 2 - and then look at what they said in Stage 2 - you voted yes at Stage 1, that means you agreed with all the details of the Bill, so these amendments are rightfully defeated - that is openly undermining the democratic process of lawmaking.
If passing a Bill at Stage 1 meant no major or minor detail of the Bill could be amended, why would there be a Stage 2 at all? The express purpose of Stage 2 is to send a Bill back to the drawing board if lawmakers (in this case Scottish MSPs) feel that a Bill has flaws that need to be corrected.
By arguing that Stage 2 is not for that purpose, ScotGov is indeed undermining democracy.
Or another example, for the Hate Crime Bill, ScotGov (or more likely the Committee responsible for the Bill) organised a number of public stakeholder meetings, where civil servants listened to concerns about the Bill from various stakeholders, all sat around round tables in groups. These meetings were openly advertised and anyone could sign up if they wanted to contribute. (I took part in one such meeting).
Despite holding three separate consultations for the GRR Bill, no such stakeholder meetings were ever organised. When women organised public meetings themselves, and complained about having to get security because of threats and aggressive behaviour from trans rights activists, ScotGov did not remind the public that anyone had the right to take part in a public consultation on a proposed law reform. They couldn't even be bothered to support a motion asking for MSPs to agree that women in Scotland should be able to meet to discuss their rights without being subjected to silencing tactics, intimidation and violence.
That's also undermining the democratic process.