A student of mine is developing a Thief mechanic for Minecraft, and I had the same discussion with him about how if I (not being a thief in the game) have my house, and my locked/protected areas, when I come back online, and find all my diamonds are gone, would be highly annoyed, and grumble at the admins. If nothing satisfactory was done, I would stop playing.
However, instead of leaving the decision there, I said that it was only my initial opinion, and we sat down and discussed it for a while, on how to keep the fun involved. What we ultimately decided, was that it could be done, and still be fun.
1) Thieves don't just steal from protected player areas, but also from vaults, banks, and stores in the game.
2) Players can take extra precautions to protect their items, but not completely.
3) Players can purchase insurance for the items. Essentially, just an insurance they drop money into, and then are given an insurance credit of up to 100 times the amount they paid.
4) If a player comes online and find somethings missing, they can make an insurance claim (simple command, no admin intervention) and if any player stole anything from their inventory within in the last 30 days, then it lists the stolen items, and they can use their insurance credits to automatically refill their inventory.
5) If a thief is caught, in the act, or via an insurance claim, a bounty would be put on their head. PVP is enabled against that player, and anyone can go after them to claim the bounty the bounty is equal to the total amount the player stole in value, even if the insurance didn't fully cover it.
6) once a player is taken out for a bounty, their inventory becomes open to the player who killed them. They may then select what they want, up to but not over the value of the bounty. The rest of the items go back to the thief.
7) a thief's skill raises the more they do it, and the higher their skill, the less likely a claim will identify them as the thief. The insurance still covers anything stolen, but the bounties on the thief are reduced or do not happen at all.
This means that the player who had stuff stolen can go after the thief them selves, and then not only do they get everything recovered from the insurance claim, but they also get the value back again from what the thief was carrying on them at the time. Added a fun extra challenge without too much loss to anyone.
In regards to a thief's guild, and limiting the number, One way to limit it, is to make other areas more enticing in ways. For instance, let it be known that taking up a Thief's role, could get them caught, and lose their stuff to any bounty hunter or police class player.
Perhaps for your first idea, you could also make it so only "free" members can have their stuff stolen. That once you pay to play, you can't be stolen from. (enticement to pay perhaps?)
However, theives pay to play premium is probably a bad idea. Once a player is paying, they are probably willing to pay for more than just thief class, like better weapons/armor, etc... a paid thief will probably be more annoying on their ability to burgle and get away with it. However, considering the bounty idea from above, you could probably do it.
Another thing you could do is keep the idea above for how to use bounties with thieves, and double the bounty for what they stole. half goes to pay off the insured player (if they are insured) and the other half goes to the bounty hunter. This means the thief always stands to lose twice what they try to steal. Making it a risk to try.