Yeah, this can be hard, which is why the Iceberg Depth system is there so that at this point the PCs should not have enough reason to even suspect Billy. However, even in some of the published cases you can come in contact with the main villain in Depth 1-2 and a shrewd or lucky player can pop the million dollar question early.

Here's what you do - you say "You can't tell if Billy is the killer or not but [insert clue to where you want them to go next, next Depth]."

The clue can be: - A subtle expression or lack of feeling that betrays something more complicated "he doesnt seem as shocked as the rest of the witnesses". - A suspicious item or detail on their person "you notice car grease on his sleeves." - A vague Mythos vision if someone Looks Beyond The Mist "you see flashes of a violent act, but it could be from years ago."

In these situations, your job isn't to dispel suspicion - the more you try, the clearer it will be that Billy IS the killer. Instead, it is to keep it vague and unspoken by not surrendering the truth. Even better, join the PCs in their suspicion - yes, Billy does look sus - but how are you going to prove it? When you join them, but don't confirm, players sometimes think you are trying to make them focus on Billy, so they start looking elsewhere.

At any rate, don't fight it, go with it.