The Equality Act doesn't have any provisions about discrimination based on marital status, other than those relating to employment. So we can agree: at work, married are protected, single are not: outside work, neither are protected.
That leaves only the question of whether 'anti-cis' discrimination is illegal. I think not, because if the Act was intended to protect everybody without a particular protected characteristic, other than from perceptive or associative discrimination, Explanatory Note 59 would have said so - it's too important to omit.
For example, if I have a justifiable occupational need to preferentially employ a trans person, how can I avoid illegal discrimination using Schedule 9? This Schedule has two asymmetric exemptions:
One: exceptionally permissible to preferentially employ a single person, but not to preferentially employ a married person. We agree(albeit for different reasons) that the latter exemption is unnecessary.
Two: exceptionally permissible to preferentially employ a cis person, but not to preferentially employ a trans person. I consider the latter exemption unnecessary, but you have said that it's been left out deliberately. Why? 'Cis' isnt even a protected characteristic, so why is anti-cis discrimination so important that it can't even be excused in the service of an occupational requirement (this is a degree of protection otherwise only afforded to disabled people)?
In any case, people do preferentially employ trans people, it's an obvious public good, and no-one has ever sued. I'm going to continue to assume that this is because it was never illegal discrimination in the first place.
So, if Newnham rebrands itself as a single-sex college that exceptionally lets in a few lads, Derry Girls style, it doesn't need to worry about the rights of the ineligible cis-male would-be candidates. (Only its founding instrument, the college statutes, and the meaning of the word 'exceptionally'.)