In the end, the added cost of the drive is worth it compared to the time you’ll save by not working in HDV. If you can, I’d highly recommend not cutting in an HDV timeline to begin with. Transcode the footage to ProRes or Apple Intermediate Codec (though the latter is still a 4:1:0 compression) on capture or through Compressor afterwards. Your storage requirements go up, but you’ll avoid problems like this in AE and the dreaded “Comforming to HDV” progress window in FCP.
(Also, Command-Shift-3 and Command-Shift-4 are your friends 😉