This version of the budget is entirely Harper's fault.
Remember that the Liberals initially drafted a budget that was far more favourable to the Conservatives than the NDP or Bloc. Harper said at the time that his party would not oppose the budget to bring down the government, and that he was pleased with many aspects of it.
http://www.cbc.ca/story/canada/national/20...tion050223.html
It was only after some of the more shocking testimony at the Gomery Inquiry, when Harper saw that the Liberals were hurting in the polls, that he decided it was politically advantageous for him to force an election.
Layton only stepped in with his offer to support the government in exchange for his proposed amendments to the budget
after Harper flip-flopped and said the Conservatives were now going to oppose it. Bill C-48 would never have existed were it not for Harper changing his mind and deciding to vote against C-43.
So if Harper isn't happy that C-48 passed, he only has himself to blame. His failed attempt at political opportunism is what led to the Liberal-NDP coalition.