I've thrown together code using Cci-Metadata to strong-name an assembly after-the-fact.
It's part of the toolset we're building for our project, but the relevant code can be found in the https://github.com/coapp/developer.toolkit inside the publishing\PeBinary class.
It's not the absolute most-elegant, but it seems to be doing the job. I've got it picking up the dependent assemblies, and handling those automatically too.
I essentially just took the source from the PEtoPE sample and started tweakin' :)