The suspect that was questioned and released- that was due to an "airtight alibi" correct me if i'm wrong. Exactly what kind of alibi was it? There have been cases before of people being released due to alibis yet they turn out to be guilty. If the person is in the military, then we're not sure with what rank he is or anything yet. If he is a higher up, the tighter close on information released is going to be. Then we still have NCIS working with local LE and i'm not sure how information sharing on the case would work exactly.
I think he was hiding in the house and had got through from the backyard. For someone in the military, they certainly would have the training to go unnoticed. The thing i question is, when Meghan left to get mac & cheese, at that time the perp could have risked his chance. Did Meghan call the neighbor first to ask if she could borrow it or just go over? If the perp was hiding in the house and heard Meghan speak aloud of her plans then he knew she'd be back. Whoever it was knew the schedule of her family that day so knew that there would be time to bind her and murder her and Lord knows whatever else.
As for a silencer, i wouldn't rule it out altogether if a gun was used. Depending on exactly who the perp is, he could have access to them or the knowledge to make one.
Whoever the killer is, he's very organized. I would lean more towards that she was strangled, as that would make the least mess than a shooting or stabbing. How long was LE inside the house for before they let her family back in? If it was a shooting, you would think they would have ballistics inside and all.
If she was bound, was the bindings something brought in by the killer from the outside or was it something he found in the house and used?
The storm drain; if she was sexually assaulted and the killer used a condom then flushed it would it get to the storm drain? Did LE pull an envelope out of the storm drain or would they have been in the drain and placed evidence into an envelope as to not damage it?