Rape seems to be a crime that is very difficult to deal with, legally, especially when the two parties are in some way or another involved. Assuming there is no video evidence and no medical evidence (i.e. injury), the rapist can always claim the sex was consensual, and assuming the two know one another (as is often the case), the idea that they might have sex is always possible; this makes it relatively easy for rapists to defend themselves.
Rape can, furthermore, be used to horribly smear somebody's reputation, cause them to lose their job and ruin and relationship they might be in at the moment - and though it is difficult to prove, it is also very difficult to disprove, except by having a convincing alibi. If two people have consensual sex, and one party decides to claim they tried to turn down sex but were raped, there is little the other party can do to defend themselves.
Assuming innocence until proven guilty could let rapists walk free, but assuming guilt until proven innocent could get innocent people sent to jail and registered for life as sex offenders. Proof is often sketchy, at best, and rape trials tend to bring out the worst in social prejudice against women, against men, against race or religion. Given these difficulties, can we really maintain normal legal procedure in cases of rape? What would the best, fairest way to deal with this problem be?