If the accused need to prove that they received affirmative consent, and it's illegal to record the consent, there aren't many options available. But a waiver is problematic because consent can be withdrawn at any time before or during sex, so it's either not a full defence or can be used as a defence when consent has been withdrawn.
How is one supposed to defend against a claim of rape when one has received affirmative consent?
The same way one is supposed to defend against a claim of theft when one has received affirmative consent to take someone else's car for a trip across town. The same way one is supposed to defend against a claim of forgery when one has received a signed check. The same way one is supposed to defend against a claim of vandalism when one has received permission to trim a neighbor's hedge that is obstructing one's view of the street from one's driveway.
This doesn't actually answer the question. These cases are crimes, and the presumption of innocence applies - the first line of defence against such claims is the knowledge that the accuser/prosecution would have to prove their claims beyond reasonable doubt. Any of these mitigating factors only need to reach the level of reasonable doubt, not a preponderance of evidence. And if you took any of them to your university instead, you'd get laughed in your face and directed to the courts/police.
No system will shield you from evil people lying to the police about you. That doesn't mean we have to endure rapes on campus, especially the ones that can be prevented when everyone knows they need genuine, honest-to-dog, affirmative consent before they engage in sex acts with someone, not just drunken or reluctant acceptance of their advances.
So if your only objection is that you want colleges to use the preponderance of clear and convincing evidence when determining if someone has violated the Student Code of Conduct and should be expelled, I agree with you. The evidence should be both sound and sufficient. But if you're arguing that affirmative consent won't keep bad people from filing false rape charges, well, of course it won't but that's no reason to allow rapists to keep on raping students, is it?
Universities are not currently allowed to use the standard you want. This is a problem, is it not? It's also not that affirmative consent "won't keep bad people from filing false rape charges", it's that affirmative consent, in combination with the removal of the presumption of innocence and prohibition of recording consent, makes it virtually impossible to defend yourself against such a claim. The rather weak suggestions offered so far seem to confirm that. "Get a new set of friends", "become a better lover", accept you'll be found guilty but hope for leniency, don't get accused of rape.
I think a lot of people are endorsing the punishment of the innocent, by arguing on behalf of sexual predators and suggesting students who report rapes are liars.
I'd like to see any examples of that. Nothing I've seen so far seems to be "arguing on behalf of sexual predators" or calling those who report rapes "liars". There are people defending the accused, and the presumption that the accused are "sexual predators" is precisely why they need defending. It is not punishing the innocent to expect rape claims to have to be proven. It's the "preponderance of evidence" standard that requires you to find that a rape did or didn't happen. Higher standards give you the option of saying there's not enough evidence to support the claim without suggesting it is false.