Yup, the only way to combat this as a smalltime dev would be to turn off auto updates and make people build from source.
However much the code is hidden and obfuscated, some parts of the source code are going to be looked upon.
For a binary, none, ever, except in the extremely rare case that someone disassembles and analyzes one version of it.
The fact that open-source doesn't coincide with security doesn't mean that it isn't beneficial to security.