The guidelines in no way mean 'guilty until proven innocent'.
The question they're planning on asking is so basic, so obvious, and (for anyone who respects their sexual partners) so simple-
How did you know that she consented to have sex with you?
Innocent men will have nothing to fear because they'll immediately answer 'I knew she consented because she said (or did) x, y,z.' And if they're telling the truth, their story will stand up under cross examination.
Not that they'd be likely to face accusations of rape anyway, because women who have fully consensual and (hopefully) enjoyable sex very rarely accuse their partners of rape.
The only men who need to worry are those who don't bother to find out whether a woman really wants sex before penetrating her. Oh and those who rape women who are incapacitated and can't consent.