I've bit the bullet and made a patcher. Should have really made it in java, but it's not my platform of choice and I wanted to play around with different nugets.
Here is the first dirty version that worked for me: https://dl.dropboxusercontent.com/u/12898517/ClickfixPatcher.zip
1. Drop into .minecraft\versions\$$versionid$$ (e.g. .minecraft\versions\16w36a)
3. Patcher should create new version 'release $$versionid$$_clickfix' with autorepair disabled and necessary .class patched
e.g. .minecraft\versions\16w36a_clickfix, visible as version 'release 16w36a_clickfix' in the launcher
4. Select the newly created clickfix version in launcher
If you want to redo it in java - do it, the logic is pretty simple, and it will be a lot more convenient for everyone.