The difference is that fixing an iPad won't require a repair shop; it'll require plugging it into your computer, which will go through its normal syncing cycle of backing it up, then upgrading apps—but it'll notice the invalid app checksums on infected apps and overwrite them with App-Store-canonical versions. If kernel-level viruses become prevalent, it'll simply start checksumming that too, and offering to restore from an IPSW with all your data (but nome of your config) intact (but that won't be a problem, since part of Apple's aesthetic is "low configuration.")

Interestingly, it'll mean that only jailbreakers—and those with no access to a computer to sync with—will ever have viruses for more than one sync cycle.