Você pode de fato corrigir isso na configuração do Apache. Adicione as seguintes linhas (e assegure-se de que o mod_mime esteja ativado):
AddType application/vnd.ms-word.document.macroEnabled.12 .docm
AddType application/vnd.openxmlformats-officedocument.wordprocessingml.document docx
AddType application/vnd.openxmlformats-officedocument.wordprocessingml.template dotx
AddType application/vnd.ms-powerpoint.template.macroEnabled.12 potm
AddType application/vnd.openxmlformats-officedocument.presentationml.template potx
AddType application/vnd.ms-powerpoint.addin.macroEnabled.12 ppam
AddType application/vnd.ms-powerpoint.slideshow.macroEnabled.12 ppsm
AddType application/vnd.openxmlformats-officedocument.presentationml.slideshow ppsx
AddType application/vnd.ms-powerpoint.presentation.macroEnabled.12 pptm
AddType application/vnd.openxmlformats-officedocument.presentationml.presentation pptx
AddType application/vnd.ms-excel.addin.macroEnabled.12 xlam
AddType application/vnd.ms-excel.sheet.binary.macroEnabled.12 xlsb
AddType application/vnd.ms-excel.sheet.macroEnabled.12 xlsm
AddType application/vnd.openxmlformats-officedocument.spreadsheetml.sheet xlsx
AddType application/vnd.ms-excel.template.macroEnabled.12 xltm
AddType application/vnd.openxmlformats-officedocument.spreadsheetml.template xltx
Isso garantirá que o Apache envie o tipo MIME apropriado para o cliente, e o IE entenderá que os arquivos são documentos do Office e não zips.