lower your reputation with the guild?

No! So feel free to tell the questgiver to shove it until he offers you something you like.

You only lose rep for:
1. Failing a quest (-2)
2. Time (-1 each month)
3. Doing quests that betray the faction (up to -20!)
And you get rep for:
1. Completing a quest (+5)

So you see it's actually very easy to stay afloat, and even failing a quest is really not that bad at all.

thanks, it actually doesnt work with the royal quests.

I once refused to deliver a kings sword and when I spoke to him again he told me I was a scoundrel. How do you raise you rep with the royals?

Royals are asses by default. Declining the quest from them does not decrease ya rep with them. Reload and talk to the Noble just to get the quest. If that Noble is being hard-headed, there always another Noble near by that offers the quest. Just remember that failing a Noble's Quest isn't a good idea.

As for raising ya standing with the Nobles, do their quest or join the local Knightly Orders (like ya have to be a Knights of the Rose to raise some rep with the Nobles of Wayrest and so on). Ya can only join 1 Knightly Orders, so keep that in mind as well.

Well, that's because nobles aren't a guild. They are like merchant quests, where the questgiver is not just one person. Sometimes a merchant or noble will have a quest, and sometimes not, but you can find them by asking around for work. Guild questgivers, however, always have quests, so refusing them is no problem.

After some time of doing quests for other factions, I returned to the Knights of the Dragon and suddenly found myself kicked out. I don't remember failing any quests for Knights, and according to Dagrep, KotD don't have an enemy faction that I might lower my knightly rep by doing errands for them. I also haven't abandoned them for long enough to lower my rep naturally this much ( < -40! ). What sort of action could be perceived as "betrayal"?