Peter Riddell thinks the whole episode has been a mess:
Ministers failed to appreciate that they are no longer trusted when they claim that the powers would not be used to pass “highly controversial” measures limiting civil liberties. First, this does not meet criticisms about inadequate scrutiny and, secondly, there is nothing to a stop a future government from using these powers.
But even if the tone of the criticisms was over the top, the thrust was correct in demanding that the letter, and specific provisions, of the Bill should be consistent with the stated aims. Ministers have responded, but only after fuelling suspicions and wholly avoidable misunderstandings.
UPDATE: Spyblog is not nearly as sanguine about the amendments.