If this is an OO-based module, you could pass a protocol version to the constructor. (Kinda like many file formats include a version.) If it's not, you could write your own import sub and use use module "1.0.0"; instead of use module 1.0.0;. This would be a bit error prone.
And if you go this route, the first version that handles protocol/API/etc. versions should assume that "no API version given" is a valid input that means "the oldest version that did not know how to handle API versions", for the sake of backwards compatibility.
