Don't know the control in FCE but a video and audio are linked when you apply them into a timeline in FCP. You can either have the setting unlink them or you can highlight it and "Apple+L" to unlink. Now you can delete the audio.
Also, you can lock the audio tracks so when you drop the video into the timeline, only the video goes in and the audio doesn't
You could also drop both in, and just reduce the audio of the video track all the way down so even though it is there, it is essentially muted. Or like Lethal said, you can mute individual tracks in your timeline.
You can also copy and paste audio from one quicktime to another in quicktime player. Open the audio track, select the whole thing and "Command+C". Open your video in quicktime, select the whole thing and "Command+V". This will put the new audio track into the video. I know you can do this in Quicktime 7 but not sure in quicktime X. I had to do this a couple times, where during export from FCP I got good video but glitchy audio. To save time, I rexported just the audio from FCP and added it to the video since it was the same edit.
There are a million ways to do this. Some are free, others cost money. It's very simple if you know what you are doing.