Had she subconsciously wanted to hurt him for lying to her?
Yes, which is why she should just have yelled at him earlier.
She thought she had been protecting him from Lex; instead, what Clark really needed was protection from her.
Exactly, she has hurt him way more than Lex ever could. Lex might be able to hurt his body, but she has ripped him to shreds emotionally.
Clark was the kindest soul she had ever met, and he was funny too.

that she has cut herself off from him.
Usually, when Lois wasn’t stressing him out too much, he was a good listener.
See, she should really have avoided the M word at all costs.
How could she have expected a man whose heart she had just crushed with the news that she hadn’t flat out refused Lex’s proposal to have been able to listen properly?
Exactly, she really should have thought this through better.
She had been jumpy, nervous, and scared of her own shadow, worried that she would never make it to her rendezvous with Clark,
She really should have had Superman come and whisk her away to an undisclosed secret corner of Metropolis.
and frightened that one of Lex’s men would steal her off the street before she could tell Clark what was going on.
She really is in too deep.
She hadn’t been thinking straight. When Clark’s proposal had come out of left field like an attack, she had defended herself.
That was the stupidest thing she could have done. She should have tried to see things from his perspective.
Lois didn’t know if Clark would ever forgive her.
Why should he. He bared his soul, and then had her come and rip it to shreds.
She did know, though, she wouldn’t blame him one bit if he never did.
OK, I am just too mad at both of them for being total lunkheads. I just knew something horrible would happen when she went with her stupid undercover plan. I am feeling perturbed at everyone. I am trying to not be too put out, but I am just discouraged with things.