JavaScriptCore (like other js engines) has an interpreter and a JIT. The JIT requires memory that's both writable and executable. iOS doesn't allow memory that's both writable and executable for security reasons, so normal apps can't use the JIT parts of jsc. Safari gets an exception from the "no writable and executable memory" rule.

(That's the technical reason; if you're wearing a tinfoil hat, you could argue that Apple wants to make sure native apps work a lot better than thin UIWebView shims, for lock-in and whatnot.)