You can manually add module.exports = window.$
to the bottom of the zepto file or use browserify-shim in order to get your modules adapted for browserify on the fly.
I would recommend the latter option since editing 3rd party modules is problematic especially if you plan to upgrade them later.
browserify-shim was tested to work with zepto in particular.
Take a moment to study the readme and examples to learn how to properly set things up. You can then of course shim pretty much any library that attaches a variable to the global context, i.e. jquery.
On another note, the errors you got where due to a bug in browserify that has been fixed in the meantime.