It's not just that Boehner and McConnell hate Obamacare and it's not just that they're hypocrites about spending. What they're saying with their actions is that if they can't convert Medicare from a single-payer into a private insurance system, they'd rather the whole thing collapse under its own weight. President Obama's and Paul Ryan's Medicare plans both envision budget caps for Medicare -- the difference is that Ryan wants to let private insurers enforce it while Obama leaves the task to providers, with IPAB as a backstop. The parties are actually in about the same place fiscally with respect to Medicare, but unless reaching a more sustainable trajectory means privatizing the program, Republicans will try to keep it unsustainable.
Unfortunately for them, the story's not that simple. The GOP can't straightforwardly nullify or hobble IPAB by withholding or blocking nominees, the way it can and does with the Consumer Financial Protection Bureau and the National Labor Relations Board. The IPAB can seemingly function with fewer than 15 confirmed members, and even if Senate Republicans filibuster all nominees, the ACA includes a backstop that basically allows the Health and Human Services Secretary to act as a one-woman payment board. So just as states' rights-loving governors are ceding their sovereignty to the federal government instead of setting up insurance exchanges of their own, Boehner and McConnell are effectively handing power to the executive branch in lieu of doing what the law asks them and maintaining influence over the policy.
Now that may not be a power that the Obama administration wants to exercise. And its not one that'll necessarily remain in Democratic hands forever. So it's not a perfect alternative to IPAB. But it's also not a win-win for Boehner and McConnell. The GOP base might appreciate it, but it's probably counter to their substantive interests.