/hɑːmɑːˈtiːə/ is how I would have pronounced it, but I wanted to make sure if /həˈmɑːʃə/ existed as an alternative. LPD3 keeps schtum; ODP proposes /həˈmɑːtɪə/; EPD lists /ˌhɑːmɑːˈtiːə/; Merriam-Webster Online has /ˌhä-ˌmär-ˈtē-ə/ (which is the MW way of transcribing /ˌhɑːˌmɑːrˈtiːə/.
Hamartia or tragic flaw is not a concept that you discuss with your Significant Other every other day. In literary studies, however, it does pop up every now and again. I think I ought to take the professor aside and tell him how to pronounce the word.