As a nation founded on immigration, and the displacement of Native American peoples, the use of the term "Homeland" is disingenuous at best, and jingoistic at worst. "Homeland Security" implies an anti-immigration and anti-foreigner bias. "Homeland" is a term which recalls similar phrases used by some of the worst regimes in history, such as the Nazi "Fatherland" and Soviet "Motherland." The term is recent in American usage, dating to the most recent Bush Administration which advocated an aggressive foreign policy, and has no longstanding history to counter its negative connotations.
Valid other alternatives exist to cover the mission of the current agency, such as "Domestic Security" or "Civil Defense." "Civil Defense," in particular, recalls the service on the homefront in WWII.