これらすべてに加えて、IsActive=1のレコードのみを選択できるようにする必要があります。
SELECT DISTINCT 0 as CommunityID,
CASE Libname
WHEN 'RKHL' THEN 'ROCK HILL'
WHEN 'FTML' THEN 'FORT MILL'
WHEN 'LANC' THEN 'LANCASTER'
WHEN 'BREV' THEN 'BREVARD'
WHEN 'PBTC' THEN 'MIDLANDS-CLEC'
WHEN 'PBTI' THEN 'MIDLANDS-ILEC'
END AS CommunityDesc,
LibName,
LibName + '|' AS FilterByID,
IsActive
FROM Reference.dbo.Community
WHERE LibName <> 'CAROTEL'
UNION
SELECT CommunityID, RTRIM(COMMNAME) AS CommunityDesc, LibName, LibName + '|' + RTRIM(COMMNAME) AS FilterByID, IsActive
FROM Reference.dbo.Community
WHERE LibName <> 'CAROTEL'
ORDER BY 1,3;