Q: Is it possible to encrypt my operating system boot partition?
A: No, TrueCrypt does not allow this. However, there are ways to ensure that the volume where operating system resides is read-only, which should prevent information leakage (registry, temporary files, etc., are stored in RAM) and make it impossible for an adversary to install a Trojan horse on the system. One of the ways is using BartPE. BartPE stands for "Bart's Preinstalled Environment", which is essentially the Windows operating system prepared in a way that it can be entirely stored on and booted from a CD/DVD (registry, temporary files, etc., are stored in RAM - hard disk is not used at all and does not even have to be present). The freeware Bart's PE Builder can transform a Windows XP installation CD into BartPE.
If you use TrueCrypt 3.1 or later, you do not even need any TrueCrypt plug-in for BartPE. You can simply run TrueCrypt in 'traveller' mode under the BartPE system from a BartPE disk itself or from any other location where the TrueCrypt system files (i.e., 'TrueCrypt.exe', 'TrueCrypt.sys', etc.) are stored. The type of the CD or DVD on which you store BartPE should be "write once, read many" (for example CD-R), because rewritable disk types (such as CD-RW) might allow an adversary to alter the contents of the disk.