If it won't accept an arbitrary codec between two SIP endpoints, your best hope for fixing this would be the SIP Device Capabilities form but I've had a look and I'm not optimistic. As you say, media does not traverse the 3300 so it shouldn't care [or you should be able to tell it not to care].
Failing that, can the extensions be configured to use a second "line" to connect to each other back-to-back?