So first, I installed the Lockette plugin. You can now lock chests and doors. There's a little bit of permissions to work out, but for now it should work fine for most cases. I'll update the Original Post with a link to a video explaining how to use it.
So I'm gonna explain what the logs show. So technically Tybalt and Grape aren't the ONLY ones who logged in to the server in the last 24 hours before the incident. Here's the explanation.
First of all, a few facts
1. Nobody warped to St.Mary, there hasn't been a St.Mary warp for a few days prior so people must of either walked there, or spawned there automaitcally (or had their /home there)/
2. I discounted the times when multiple people were on at the same time, there were periods where 3 or 4 people were on at the same time but they were tping to each other and /warping to locations far away from St.Mary's, so I figured these times were unlikely to be when the grief was caused cause everyone was together.
Now for the five (yes there is a third) people who are under a bit of suspicious.
1. Grape logged in several times when no one else was online and he didn't warp anywhere, he had a very used flint and steel and admitted to doing small destruction to a horse and chicken farm in St.Mary, but denies doing the majority of the destruction. Note: Apparently there was an incident with horses and flaming stuff that happened.
2. Tybalt logged in a few times, he's been seen with diamond armor which is odd for someone whose only joined for a bit, he's also been accused of stealing from chests and so forth so is a suspect.
The rest are rather unlikely:
3. aperson logged in and warped to St.Mary, however he was warping to every warpable location and only stayed in St.Mary for about... 10 seconds, as well this was about 30-40 hours after it was discovered, so it's unlikely aperson caused it.
4. Nic. Apparently Nic was in Hillside with Alistar or something and spawned horses and chickens but they didn't seem to cause any damage (Note: This was probably related to the incident Grape was talking about before). However, curiously, at about 3 hours before it was discovered, Nic did go online and "burn to death" but it was impossible for him to be anywhere near St.Mary at the time because of his previous warps. So I think Nic is unlikely too.
5. Alistar was on a lot of times by himself. The reason I don't really think he did it is because everytime he logged on, if there was no one on he'd log off about 10-15 seconds later. Anytime someone else was on he'd immediately teleport or move towards them, so it's unlikely he was able to cause the destruction at that time.
The only person I haven't heard from is aperson