I think Clark's journals were a good move. I had been thinking some of the same things that Clark expressed about him taking the stand: he would be in the same room with Lex, who would try to manipulate him and get in his head. I'll admit that I hadn't actually considered that Nigel or Mrs. Cox might be in the audience with Kryptonite. That actually sounds pretty likely.
One thing Clark doesn't seem to have realized is that him coming forward at all means that the authorities will need to know who he is. He does have a birth certificate and legal identity, even if he wants to distance himself from it. (He could always legally change his name once the trial is over.) Him being Kal Luthor is integral to how Lex manipulated and abused him.
Lex giving him the name "Clark Kent" is kind of weird all around, since he didn't let Clark interact with anyone, except that it serves to distance Kal from Lex as his brother, but Clark doesn't seem to have noticed that.
All in all, "Kal Luthor" will need to be the one to come forward and testify, and then he can be declared legally alive. I can see why Clark would want Lois' contacts to make him a new identity from scratch to try to distance himself from his past, but he doesn't actually need to do that in order to have a legal (alive) identity.
You are, of course, right. But Clark's not thinking straight. And Lois is willing to do whatever it takes to get Clark free of his old life.
And you're very right in that Lex is distancing and destroying the identity of Kal Luthor and any ties Clark has to him as a brother. He doesn't really want Clark thinking of himself as his brother (note that Lex never calls him brother when speaking to him). He wants Clark to forget he was ever a Luthor as he twists him into his own servant.
I think it's extremely likely Lex would plant his own assassin in the courtroom (or even more likely, outside of it) to kill his super assassin. Clark is way too much of a liability to him.
