Your son's lawyer is only doing his duty in telling him that he will get a discount for pleading guilty. That is not telling him to plead guilty. Where do you get any idea from that having clients plead guilty, when they're not or when they are, makes the solicitor more money? He's going to get a jury trial out of it, and several days in court, on a fight, as against an hour in court on a plea of guilty, plus the extra preparation time for the trial. Which do you think earns him more?
If the CPS thinks it's worth proceeding with they must think that not only is there a prima facie case, but it's a case which appears to have a probable chance of resulting in a conviction and one which it is in the public interest to prosecute. That is so whether its one man's word alone as the basis of the case, or twenty witnesses including the Archbishop of Canterbury, two doctors and forensic science experts. It'll be up to your son's solicitor and counsel to show that that confidence was misplaced.