Yes the Patriot Act and the NSA PRISM project will be issues in both primaries, but it is quite probable that both candidates will be for re-authorization so it wont be an issue in the general.
The media will see to it that both nominees support it.
And by that you mean "Rand Paul won't be nominated". (or any of the other 48 senators who voted against it)
I do think the fact that Paul is at odds with the "party establishment" on both foreign policy and civil liberties issues is a pretty big impediment to his chances at winning the nomination, yes. Not that him winning the nomination is impossible. But it seems awfully difficult for him if he doesn't compromise further on those issues than he already has.