OK, I solved the problem on my app by recreating a blank meteor project, carefully copying all code, asset and db files into the new folder, then reinstalling Meteor and npm packages.
Before reinstalling any Cordova plugin, I tried to deploy a build to iOS : it worked without problem. Then I reinstalled all Cordova plugins one by one, and noticed Xcode started to raise the Apple Mach-O Linker error again right after installing a specific plugin : phonegap-plugin-push.
But this time, the workspace workaround mentioned by @themuffinman worked again and I could deploy my app to iPhone.