Are you talking about flash embedded in the mcu, or separate flash chips? The mcu can usually reflash itself, modulo fuses, but I can't recall having seen a standalone flash chip which lacked a write protect (or write-enable) pin. A physical toggle switch on that line seems like a solid protection against NSA style firmware hacking.
Unless you're talking about a pin supplying a required programming voltage, that WE pin is just hooked up to internal gates that suppress writes. There are relatively easy ways to back-door gates (e.g., with secret access patterns or data sequences).
