I think it's supposed to be ambiguous. I think it's more likely that the halfway house guy killed Dr. Black because he came back for more serum and there wasn't any, because Lex had taken it — and that Lex's ominous "I can't allow you to do that" threat was just preparation for him not letting her destroy the serum. I buy that interpretation because if Lex had prompted the kill, the halfway house guy would have been next, Lex wouldn't have let him be arrested and possibly talk, not if Lex already had proven he wasn't above murder.

I agree that Clark's being careful and trying not to rush to judgement (and it's so hard for him not to, poor lamb! ;-)).