Hi Lee,
Great question and the first time I have heard this asked. :) First off, I recommend against full trust. Full trust complicates deployment. If, as it sounds, you have already, jumped those hurdles, then the code signing certificate will have to be renewed and reattached to the form which means you will have to republish when it expires.
Users use different digi-certs to sign forms. Those will not be affected by template changes. I am actually surprised to hear that you say the template cannot be upgraded since it will invalidate the existing forms. Not sure I follow that logic. Auto-upgrade should work. Signing the template only affects security of the template, not of the data. So, I think this is a red herring.
If you can remove the full trust requirement that would be best. Otherwise, I think the MSI is more work since it requires an install whereas the digicert has a more web-automated install. It's 6 of one / half a dozen of the other. Not sure you can say which is better. MSI is cheaper since you don't need to buy a code signing cert.
Patrick Halstead [InfoPath MVP]
InfoPathDev
Patrick Halstead
Project Manager at Qdabra