I think you're right. But whichever way you cut it, it's inexplicable and unforgivable that the police didn't test a strange stain on a pillowcase that was underneath the victim of a murder with sexual elements. I've heard it said that perhaps the police figured the stain might be Silenzi's (Meredith's new Italian boyfriend's) semen, or even that they actually did test it and found it to be Silenzi's semen. But if that were the case, this fact should have been disclosed and the issue closed off: any "explanation" along the lines of "protecting the victim's privacy" go out of the window, I'm afraid, when people are on trial charged with murder.
I personally think that the stain was Guede's semen. I think it's hard to conclude that he went to the extent of penetrating Meredith (either with his finger or his penis) and didn't engage in any sexual activity of his own. There are numerous examples of men who assault women then reach a climax either as the women is dying or after she is dead - unpleasant but true. It's actually probably a more common occurrence than that of men who rape a woman then kill her after they have reached ejaculation (after which point feelings of aggression and powerlust tend to subside dramatically). As a result, when there is a female victim of rape and murder, it's extremely common for police to find semen on a victim's body or on clothing/ground near the victim, rather than actually inside a victim.
So I think it's not unlikely that Guede initiated a sexual assault on Meredith, at which point she struggled and screamed, and as a result of which he killed her. I think that - horrible as it seems - Guede continued with the sexual assault as Meredith lay dying, and ejaculated onto the pillow. I think that post-ejaculation, his feelings of aggression, lust and a need to dominate subsided dramatically, and he realised just what he had done. I think he spent five or ten minutes thinking about his next move; then he went to the bathroom, cleaned himself in the shower (probably), returned to Meredith's room with towels from the bathroom, possibly went towards the front door then turned round and returned once more to Meredith's room to find the keys he needed to open the front door.
As an aside, I see that Barbie Clouseau says that she has received numerous death threats following her recent reporting from Perugia. Now, even a cursory analysis of her tweets since Monday shows that almost without exception she's made comments that are extremely pro-defence (apart from some late equivocation which might well have been an attempt to ward off any further death threats). I would therefore find it reasonable to assume that those sending death threats are FAR more likely to be on the pro-guilt side of the argument than on the pro-acquittal side. Still, there's a UK solicitor who has issued a stern warning which he will say once and once only, so it's all OK