You should probably do that with the .hex (it's the hex code of the microcontroller) But not sure how can you upload the code with the Arduino IDE once other people got the .hex file..
Actually I'm pretty rusty on this end of things these days and I also thought you meant at run time. You can probably compile your code to an object file then have people include that in their project at the link stage. But I don't think you could do that under the Arduino IDE, you'd have to get down and dirty with make files.
As I understand it the OP wants to provide a "module" for developers to include with their program. In other words a library but without the source code.
Is that the case? If so it can't be done at the HEX file level surely.
I need to provide updates for the micro to the UI developer in a remote location. He's not an embedded developer and has no need to see the source code. He just needs update to functionality as they become available.