Maybe he was relying on Valera's story casting reasonable doubt on the possibility of Natalia being the killer, and buying his team time But it actually makes things worse, as Jake happily leaps on a conspiracy charge which will get them *both* in trouble. How the hell did Horatio not see that coming? You know, in a different context, if it had been Calleigh coming up and confessing to a potential murder - setting aside that Calleigh would not fall to pieces like poor Valera, and would never be in the situation in the first place, anyway - I suspect his first reaction would have been to keep that fact under wraps for a bit while darting down to see Alexx and get a clear confirmation of CoD. At the very least, he would have been heavily suggesting the self-defense angle.
Now true, I don't really get a sense that Horatio is against Valera at any point, but I certainly don't get the sense that he's supporting her, either, not like when she was fired. Of course, back then Horatio was still human and still connected to the lab, and he took any investigation of his lab, any facet of it, as a personal offense, but at least I felt like he was trying to go to bat for her. This time he just stands above it all, an impassive judge, maneuvering the pieces as he sees fit.
Feel free to interrupt me at any point if you can explain Horatio's thought processes - I feel kind of dumb that I can't figure out what I'm missing, but I'm sure there's something crucial that I'm not grasping. Okay, carrying on.
Other things that stick out for me - Natalia gets a holding cell visit; Valera gets ignored. Natalia gets consolation at the end, and while I've fixed it in my head that Horatio at least popped his head in to make sure Valera was holding up after, uh, *ticks off on fingers* nearly being raped, narrowly avoiding it only by slamming the guy's head against the floor, thinking she killed him, feeling horribly guilty about it, and nearly sending herself to jail...we didn't see that, so it feels like he just brushed her aside, lab rats apparently falling outside his Purview of Compassion.
Also, I still cannot get over Natalia's extreme stupidity where she spies on Valera's date - claiming "oh noez, I was worried about her!" Well, then perhaps you might have a) NOT GIVEN YOUR EXPLICIT OKAY FOR HER TO DATE HIM and b) after apparently regretting that decision, COME UP WITH A SLIGHTLY MORE SPECIFIC LIST OF REASONS WHY NICK IS "DANGEROUS," such as throwing the phrase "physically abusive" in there.
And this was one of the few season 5 episodes I thought was salvageable the first time around, too. Oh, show. How did you sink to such levels of suckage?
[Edit: Oh God, just read that this episode is Eva la Rue's bid for a supporting-actress Emmy nom. Look, I'm not completely opposed to her being nominated, but THIS episode?! There was a point, where she admits to Valera that yes, she was sleeping with Nick, where I actually thought to myself how horribly acted that part was. And I never actively notice bad acting.]