I don't think this follows. If premature optimization is the root of all evil, essentially, we're saying "for all evil, there exists a premature optimization which leads to it." If evil, then sourced in a premature optimization.

Even if we parse his "But..." as saying, "there exists some premature optimization which is not the root of an evil" (ignoring probably valid quibbles about whether the optimizations he's talking about truly are premature), this doesn't contradict the original statement.

In fact, "the root of all evil" seems to be an expression which invites us to commit the fallacy of denying the antecedent -- if premature optimization, then evil, in this case -- because it is almost always used to indicate that the first thing is bad.