The solution is simple, copy a tarball of the source to CD and throw it inside the casing of the missile. Add rocket fuel to compensate for the added weight.
I think, on the other hand, that it's a very interesting thought experiment. While the realities of the original question are a bit absurd, the question does give one the opportunity to think about and discuss some interesting legal edge cases (government copyright infringement, and the implication thereof)
Further, it's fun to theorize about possible solutions to OSS licensing issues: Deliver the source via special courier (military strike team); deliver via the same means as the compiled code (a second missile); etc.
Related question: If a (non-weapon) device is shipped containing a GPL-derived program which includes a copy of the source, but destroys it on arrival, does that obey the license?
Obviously, use a micro SD card, it's much smaller and easier to stick somewhere.
Come to think of it, would that actually be heat resistant enough to allow the receiver to be able to read it? Hmm, perhaps some more research is necessary after all.
Second:
The solution is simple, copy a tarball of the source to CD and throw it inside the casing of the missile. Add rocket fuel to compensate for the added weight.
EDIT:
Third:
That was an intentionally stupid answer.