Multi-site: how to handle some module differences?
Create three modules named site1.module, site2.module and site1site2.module respectively. Store changes (hook_form_alters) for site1's forms (including those of your custom module) in site1.module, sites2's forms in site2.module, and forms of both sites in site1site2.module.

The module names will of course need to be swapped for more meaningful alternatives.