Realistically, they could not shut down Bitcoin itself, but they could sue merchants that tried to adopt it as a payment.
Well based on the patent (even as vague and likely reversable as it is) I don't see how it could have any bearing on Bitcoin. If anything Bitcoin would be the one technology businesses SHOULD adopt if Apple tried to start enforcing this.
Simple version of apple's patent is micro-transactions have prohibitively high transaction costs, so we have user buy credits (single transaction cost from fiat -> credit), then we use a more efficient system for individual purchases credit -> media. Bitcoin doesn't need credits because the transaction cost is free (or at worst in the future very low). Given consumers tend to hate buying "credits" using Bitcoins over some patented (as dubious as it is) credit system is a competitive advantage.
One example would be mp3s. Credit card companies have reduced their rates but still make about $0.15 per $0.89 mp3 sold. Using Bitcoin someone like Amazon could have a transaction processing cost of maybe $0.01 (including exchange fees). If they were willing to take half the profit margin (about $0.10) they could undercut Apple by $0.20 more.
ITunes (w/ fiat CC) - $0.99
Amazon (w/ Bitcoin) -$0.69
The awesome thing is that Amazon couldn't do it without Bitcoin so maybe they have two pricing options. $0.99 per Song by Credit Card or $0.69 per song by Bitcoin. Imagine what that would do for adoption.
Now I don't think Amazon will adopt Bitcoin any time soon but it shows the potential and the futility of Apple's patent (even if it was enforceable).