It is possible to create a version control system of cipher text. It would be ideal to use a stream cipher such as RC4-drop1024 or AES-OFB mode. As long as the same key+iv is used for each revision. This will mean that the same PRNG stream will be generated each time and then XOR'ed with the code. If any individual byte is different, then you have a mismatch and the cipher text its self will be merged normally.
A block cipher in ECB mode could also be used, where the smallest mismatch would be 1 block in size, so it would be ideal to use small blocks. CBC mode on the other hand can produce widely different cipher text for each revision and thus is undesirable.
I recognize that this isn't very secure, OFB and ECB modes shouldn't normally be used as they are weaker than CBC mode. The sacrifice of the IV is also undesirable. Further more it isn't clear what attack is being defended against. Where as using something like SVN+HTTPS is very common and also secure. My post is merely stating that it is possible to do this efficiently.