@Acretian --Its completely fine to Un-install-Re-install IIS.Reboot ..then Repair SEPM.
Un-installing IIS doesn't delete any SEPM files..IIS host SEPM's website so that it can accessble to everybody and it can connect to database etc.
Repairing SEPM re-creates the SEPM Website in IIS.
However if you had made some changes in IIS after installing SEPM they won't be retained you will again have to manually do those..like if you have changed the SEPM Websites port or anything logging info,IUSR account. etc