I need some tips concerning joining guilds.
1) Should I join guilds early, to get access to their several benefits, or should I wait until I know that I'll actually perform jobs for them soon?
The thing is, I've heard that a) your reputation drops if you don't do jobs and B) you might get kicked out of the guild if your reputation is too low. But I have never heard anything about whether there's a connection between the two, i.e. if not doing jobs can lower your reputation so much that you get thrown out of the guild?
There's no reason to join late. Your reputation drops only a point each month, which is very slow. You can refuse quests without losing reputation and go for the easier quests. It IS possible that your reputation drops if you do quests agains't the guild, but unless we are talking about the brotherood or the theieves, you can always rejoin.
2) Which temples/knightly orders are the most interesting / best fitting for a "thief" character? (By "thief" I don't really mean a burglar, but a... "special agent" or something like that. Someone who works for the Empire, but does so by being stealthy and persuasive.)
I've read the descriptions on the UESP, but I thought you veterans might have some more information about this... maybe the quests of one temple are more fitting than those of another, even though they have similar requirements. In any case, I've read that Kynareth is always a bad idea, is that really true?
All temples and knight orders have the same quests. I don't know what could fit a thief better, but you can look at what skills they train and decide for yourself. I believe all knight orders train in the same skills.
3) When is it generally safe to accept quests? How can I tell? I'm currently level 2 (and having a hard time gaining skill points for some reason), should I even do guild quests when I'm still such a low-level character? And what about the different quests from the people inside the castles? Are they more difficult, or less?
I usually do the quests my char would do from a RP point of view. You can avoid dungeon crawls for now if you know what quests lead to them, as refusing a quest doesn't affects your reputation. Note though, that refusing a quest from the main storyline essentially stops you from completing the game.
The fighters and mages guild have some very easy low level quests. Nobles have some courier quests that are basically "take this there". You just have to play the game and build experience.