You did not clearly state which kind of protection you’re asking for.
Tracking by SIM / IMEI / phone number: Obviously, you can not be signed in at a cell tower and yet insist nobody knows about it. Of course your provider knows that you are signed in. Otherwise you could not possibly make or receive calls. And of course the agencies have that information, too. The question is, is that information useful? If you manage to obtain a Librem 5 plus a SIM card without attaching you name to it, they just know that your SIM+IMEI is booked in, but not who you are. But still, they can read all your SMS text messages, listen to your phone calls and track your position with an accuracy of guesstimated 10…100m by triangulation from the cell towers you are booked in. That last part you can effectively avoid by switching the baseband chip off. That’s why you get a hardware switch for that.
Tracking by MAC address The Librem 5 is designed so it can be used without a SIM card, which means you do all your communication via wifi. In that case, if you have a really high privacy need, you might want to change your MAC address from time to time after using public wifi. But make sure to clear your browser cache, too, else it’s worthless 
Private conversations: You can use end-to-end encrypted messengers to exchange messages and make VoIP calls that can not be intercepted (given that there are no bugs and backdoors). Depending on the sophistication of the messenger, the NSA could easily / hardly / impossibly know whom you are talking to. (I think a messenger using something like Tor would qualify for “hardly”. Reaching “impossibly” might itself be almost impossible)
Tamper proof device: If you are following the announcements of Purism, you might be aware of their efforts to create laptops with a completely FLOSS bootchain (firmware, bios, TPM, heads…). For the Librem 5 they go in the same direction, but I’m not sure if there is / will be a TPM equivalent. Ultimately, all your end-to-end encryption is of course almost worthless if you cannot verify that the software is unmodified.
The NSA has lots of power, but it does not have super powers. You seem to have the impression that connecting to a cell tower basically gives them the ability to take over your device. While that is probably the case for most of the devices currently out there (including iPhones), there is no necessity for that. If the baseband chip is cleanly separated (=has no access to RAM, CPU and other devices), then the NSA can send every command they like to the chip, but it will have no effect. If, additionally, the baseband firmware is free and open, then YOU decide how to handle some of the funny commands they might send. Maybe you can send funny answers back, I don’t know. At the very least, the user can be informed about strange commands that come from the cell tower.