Exactly. There's two distinctions to be made here I think. First is that 'consequences' needs to be proportionate to whatever the free speech was - so in this context, I would say the appropriate 'consequences' for Stock to face are e.g. other academics responding to the arguments in her papers and disagreeing with her. And I mean, I'm 100% sure she would expect that and find it reasonable, because as an academic, you WANT people to engage with your work anyway. She's also offered to be part of debates on this issue before, so she isn't scared of disagreement. The appropriate consequence for publishing unpopular academic work is not to be hounded out of your job.
The second is between free speech and hate speech. There's a lot of talk about this on academic Twitter atm. I can't find the link right now, but someone's done a brilliant thread contrasting David Miller (anti-semite academic) with Kathleen Stock and how they're very different (Miller was terminated and rightly so IMO). Again I can't find the link, but someone in Brighton has been going round putting up stickers with quotes from Stock's Twitter and work where she says for example, she uses the pronouns students ask her to, she treats trans students with respect, 'trans people exist and we should get over it' etc etc. As someone else pointed out earlier, Stock is really quite moderate in this debate and I don't think anything she has said constitutes hate speech. The problem is that some of these students now think literally hearing any views they don't like is a hate crime and this is where I feel academia is badly failing students. You do not go to university to live in an echo chamber for 3 years, you go to have your own views challenged by not only other people but by yourself, to learn how to think critically and make strong arguments, not to simply shy away from views you dislike.
I really don't know how we're at the point that students feel entitled to only hear things they like to hear, but I've seen many hypothesising that the increase in fees has resulted in some kind of commercial environment where students feel entitled to 'demand' lecturers they don't like are sacked etc. I'm sure there was a poster saying something like 'we don't pay 9k a year to have transphobes in our uni' or whatever. Sorry for another essay on this - will actually shut up about it now!!