I have a JVC HD100 (720p) and I would like to supplement it with a handheld camcorder like the FX1. My question is: if I use something like MPEG Streamclip to change the 1080i footage of the FX1 to 720p, will it look like "native" 720p? In other words, will it match the 720p of the HD100?

You will want to deinterlace first then scale it down. It should look good, but how close to the other camera will depend on how you set it up in the first place.

If your going to 30p it should look perfect with just a quick deinterlace, drop it in your timeline, render and your set. 24p will be a little bit more tricky.