It's awful crypto and it made me throw up in my mouth a little bit. They should be using RSA to encrypt a random key then encrypting the rest of the message with some sort of authenticated encryption.
1. Tools to encrypt messages using Github SSH keys are probably not a good idea. They're no more usable than real message encryption solutions, but have far more constraints.
2. You cannot safely use RSA like a normal cipher. RSA is a tool for building crypto protocols. The way you've deployed it here has a serious vulnerability.
If you want to build things that use cryptography, I think you really need to work with a high-level library. Nacl (or libsodium) is a great example of a package that goes out of its way to bulletproof itself.
I'd say we need more effort on small, focus built libraries for tasks such as these. You can talk about how people need to add in Nacl into their project, but actually doing that is simply not possible for many developers.
eg, more libraries like this one: https://github.com/tozny/java-aes-crypto
If you're worried about size, use Tweetnacl:
TweetNaCl is the world's first auditable high-security cryptographic library. TweetNaCl fits into just 100 tweets while supporting all 25 of the C NaCl functions used by applications. TweetNaCl is a self-contained public-domain C library, so it can easily be integrated into applications.
I definitely do not think the proliferation of unvetted, anonymous crypto libraries is a good thing. How many people have the expertise to write this kind of thing? How many have the expertise to evaluate its quality?
For example, the documentation for the linked library says: "we've also added integrity checking in the form of a SHA 256 hash." This is a huge red flag: hashes provide integrity, but not authenticity, which is really what you want here. But then you go and look at the source code and find that they are actually using HMAC-SHA256, which does provide authenticity. So the documentation is not an accurate description of what's going on, and you need to go and look at the source to find out that it really is okay (in this particular aspect, though it doesn't inspire confidence for the future).
My point is not to say that this particular library is terrible or anything. Just that we have limited resources, and we're better off consolidating to a very small number of solutions designed, written, and validated by experts.