It's a tough situation. Encryption can be used for good or bad (and even the definition of what's "good" or "bad" encryption varies depending on who you ask). Unfortunately, I see it increasingly being used to oppress users, in the form of DRM and other "security" features.
Perhaps classifying encryption as munitions makes the most sense, if you support 2A rights.
On the other hand, it's just maths. Maths which anyone can theoretically do.
I don't know if there is a good solution to this problem.