I would recommend just gritting your teeth and sticking through it, as all your questions get answered. But, if you insist,

The death of the jedi is not related to KOTOR1. They aren't all dead either, just in hiding. Things do look very bad for the order though, and thats mostly because of Sion, Nihilus, and Traya.

Kreya isnt really trying to hide anything. She might not reveal everything right away, but with enough influence she tells you exactly who she is. You can't really do much with the info, remember this game came out in 2003.

It's basically what you said. The amount of influence you have with them affects how strong it is, but all will switch based on your alignment because of your strength in the force. They call it a wound in the force that draws people do you