The old app LiteSwitch X (Proteron Software) would allow you to selectively hide apps from the application switcher. For several years now it has been unsupported but I just googled for it and found a beta version that claims to add compatability for OS X Mavericks so it may work for you.
Back in it's day I loved using it but since it went undeveloped for so long, I had to look elsewhere (and couldn't find quite as good of a solution). I'll be testing out the new beta version myself! Until recently, the best I've found—though, it doesn't solve your problem—is Hyperswitch. Hyperswitch works great but doesn't (yet?) have the ability to hide apps.
Direct download link (LiteSwitch X v2.8b1)