Hi Corey,
I can see what sort of game you want to play. The good-guys are good-guys and (usually) act accordingly. That's fair enough. That's the sort of game I prefer as player and DM.
You need to get your players to think about the sort of game they want - and come to a compromise if that's necessary.
I suggest you speak to all of your players as a group with the attitude that they are not doing anything wrong, but are they sure this is the sort of game they all want to play? Do they want to have the sort of game where PCs steal from each other? Do they want to have the sort of game where PCs make decisions based on expediency rather than what is "right"?
Leaving aside alignment considerations for a moment - what sort of game do you ALL want to play and can you reach an agreement about that?
If your rogue/thief has a character driven story-arc is mind for his PC which explains his stealing, and if you and the rest of your players are happy to indulge that then fine. Likewise for your other dilemmas.
I suggest you develop an idea of what you are all hoping to get from the game character-wise, and outline a simple social contract based on that so that everyone is on more-or-less the same page, before you start looking at IC consequences and warnings :-)