The ACA was budgeted long-term in the original legislation but the ACA is NOT a 'non-exempt' program so it is hurt by sequestration. In particular, insurance company subsidies to offset co-pays and deductibles will be reduced. It's doubtful the government can get insurers to eat those loses, especially if they don't get enough signup in the next two months to make the exchanges look profitable in the first place.
The next year is critical for the ACA. Both for exchange customers who need to be happy or will pay the tax next year instead of premiums, and for insurers who could decide it's not worth it to participate in the exchange unless they can REALLY jack up premiums.
Rs know this and have the house for another year. That's not changing and sequestration is "the current law" until congress changes it. [Not sure about this site but it's was high on google results and covers it http://www.massresources.org/sequestration.html and covers it pretty well.]
The Rs are likely to wisen up PR-wise by the next fight (jan/feb 2014). Just like Ds have been saying "The ACA is the law, suck it Rs", the Rs are likely to come out saying "Sequestration is the law, suck it Ds". They don't like the military cuts but can loudly say "we'll fund EVERYTHING - including ACA and all entitlements - according to the current law which had bipartisan agreement." It's hard to say who will win that PR battle but there is potential big trouble for the Ds & ACA - especially if there is dissatisfaction with the ACA early next year (when people are first trying to use their exchange policies).
Obama's in a tough position. Give the Rs something they want so both sides can move forward with some of their agenda. Or have a huge PR fight potentially risking the ACA, and plan to fix all the problems after wining the PR battle and the 2014 house. The big problem is that the ACA may not be fixable after 2014 unless it gets some fixes before then (at the very least, it needs elimination of sequestration).