I wasn't aware since I hadn't tried it before, but if I give it a shot and there are no issues, it might be possible.
Of course, since it's a significant change, it would probably require internal discussion within the team. :)

I've just used the SQLite3MC amalgamation to build the dll and our project can still access a sqlcipher database. You just need to set the cipher before setting the key or password.

In fact it makes a bunch of other things less complicated, like creating a backup - you can easily use "VACUUM INTO"

I imagine using it instead of sqlcipher.dll is straight forward. Then the UI would need to be updated to enable selecting different ciphers.