Can't you use the Decklink card to downconvert the 720p/29.97 to SD NTSC 29.97 in the card?
You will need to convert in someway to avoid those tell tale black bars. Ideally, you don't want a mixture of codecs on the same timeline. Render hell will ensue. You should be able to output Quicktime from After Effects unless AE is on a PC, but then maybe even then!
We all are waiting for the day when Final Cut Pro can deal with different codecs on the same timeline. When oh when?