No need to panic, I think: By calling evidence-based medicine "just an opinion", they aren't meaning to imply that its tenets aren't true or fully established. They are only attempting to claim that it doesn't meet the standards that beliefs are required to meet to be protected under the Equality Act.
In principle, I can see the truth in this: A simple acknowledgement of a massively well-established truth won't generally count as a protected belief (my belief that my laptop is in front of me isn't protected). If such beliefs were protected, then the Equality Act would march imperiously into more or less any disagreement of fact involving employers or service providers.
This is perhaps the reason why it was so very odd that the legal manouevre necessary to establish the rights of gender critical women involved establishing that the perception of sex and its significance amounted to a protected belief.
I think the key difference, here, though, was the development of a widely accepted ideology that denied the reality/importance of sex. That ideology created the conditions for acknowledging the existence of what you might call a defensive 'shadow ideology' - namely the negation of gender ideology, with its own movement and adherents.
There is kind of a double status for sex realism. There's the original material perception of sex (and its implications), which is on a par with (e.g.) the belief that air is mostly nitrogen and oxygen. And there is the set of ideas, phrases, arguments, public expressions, etc., that women were forced into developing in their attempts to rescue the original basic perception of sex from gender ideology. The latter took on a character that allowed it to be recognised as a protected belief.
If a bunch of ideologues started to challenge the idea of evidence-based medicine, and harrass its proponents (if, say homeopaths became radicalised and rampaged around social media and NHS management meetings demanding a 'safe space' from evidence-based medicine), then scientifically-minded medics might develop a set of defensive ideas, phrases, arguments, public expressions, etc that could amount, in tribunals, to a protected belief.
I guess that in the Sussex case, the claimant is arguing that gender ideology has in fact created the conditions in which proponents of evidence-based medicine have had to develop a defensive set of ideas, phrases, arguments, public expressions, etc - and that it is therefore a protected belief