The purpose of encrypting the file system is so "attackers" can't read it. Exactly how one does this depends on which attack one is worried about.
In your case, you seem to be saying that you want the root file system encrypted, but always unlocked right after booting. OK, this implies that you are not worried about attackers who log into the running system (whether authorized login or not), nor about attackers who hack into the system and can get to the file system through the OS. It also implies that you have some defense left: If you detect that an attack is coming (for example, you see the black helicopters on the horizon), you quickly shut your machine down.
That implies to me that you are only worried about attackers who can physically take control of the machine. For example a burglar who comes and steals your computer. Or a guy with a black helicopter who comes in, sits down, and reboots the machine. Now, if you store the passphrase on a USB stick that is always physically attached to your machine, you have lost nearly all defense: both the burglar and the guy with the black helicopter can unlock your file system; all they need is the server box and the USB stick. At that point, encryption no longer makes any sense at all, just stop using encryption.
OK, it is a little more complicated. In theory, you could when you see the attacker coming take the USB stick out, and flee with it (and make sure you can run faster than a helicopter can fly). Or you could take a hammer and destroy the USB stick. But that's silly: If you have a hammer, you can also destroy the disk itself, which accomplishes the same thing.
What I'm really trying to say here is this: Security (of which encryption is a part) only works if you think through possible attacks, and how they will be handled. The boot password adds security, by requiring your body (and brain and fingers) to be physically present when booting. Take that requirement away, and encryption no longer adds any security.
By the way, this does NOT mean that I'm saying that disk encryption is utterly useless. There are scenarios where it is valuable. For example for laptops, where a human password entry is required. Usually in modern production systems, that is actually implemented using two-factor authentication: to unlock the disk requires both the human to enter a password, plus the human to have a physical item, like an encryption dongle, or a finger that matches the fingerprint scanner. That helps handle the case where the rightful owner of the password had to give it up, because they were being tortured. The other way it can help is with automated mounting, if the place that stores the passphrase is guaranteed to be secure. For example, I know of military and national security facilities that use encrypted disks (today typically using SED = self-encrypting disks, which handle security in hardware), and for automatic mounting they have a KMS = Key Management Server, which on demand distributes the equivalent of passphrases. But these places typically install the KMS hardware in metal cages that are virtually impossible to break into, and then typically station guards with machine guns in front of those cages (this is not a joke, I've worked with sites where every sys admin has an assault weapon on their back, for safety reasons). Such a setup can give you good security. Having the passphrase in cleartext on a USB stick turns security into a joke.
Finally, if you (in spite of everything) really want to do this, here is how: Don't actually encrypt the root file system, because that one needs to be unlocked during booting, and I don't know how to modify the boot loader to get the passphrase from elsewhere. Instead, encrypt only the /home file system. After all, everything other than /home just contains a copy of a FreeBSD installation. Then don't auto-mount home, but mount it using a little script that is started after booting (using cron or a rc.d service), and which first mounts the USB stick and retrieves the passphrase, then manually mounts the file system. Ultimately, it comes down to "cat /mnt/usb/passphrase | mount -o ... /home".