There are many aspects to computer security and many threats to address: poisoned DNS, worms, trojans, viruses, rootkits, firmware malware, etc. One of the biggest software vulnerabilities is buffer overruns, another is execution of user code.
Encryption does not directly address any of those threats. Encryption is a tool that hides information, which can also sometimes be used to establish trusted identities, but that is all. Indeed, if the OS you are using to encrypt a message is breached, then the message is no longer safe, no matter what encryption strength is used. As another example, if an encrypted disk contains an OS, and the OS is breached, the encryption is irrelevant and the data is breached as well.
Based on industry-standard threat models and frequency of various kinds of attacks, which is a greater risk: loss of channel security for an un-encrypted channel or loss of OS integrity due to security vulnerabilities and thus loss of encryption keys?
If a compromised OS is the OS of a server, then there is necessarily loss of channel security for the channels passing through that server. Does a secure system require both encryption and OS security of the end-points?
This question seems highly connected to vulnerabilities in Apple's FileVault. See the discussion: Potential FileVault problems in my setup