It shouldn't be difficult for the Prem/FA to sort.
If a footballer is on bail/under investigation for a disgusting crime like rape, then he's not available for selection until the charges are settled one way or the other.
Easy.
The investigation + then trial process for rape can go on for years, you think a player should be unavailable for selection for years based only on an investigation?
We need to get a lot better at investigating & convicting rapists but punishment isn’t up to the football association.