Not exactly what you're looking for, but you could just not launch iSync to begin with. In the iSync preferences, check Show iSync in Menu bar. You should see the arrows icon appear. Now you can quit iSync. Whenever you want to sync, just go the iSync icon and select Sync Now.
Syncing will be built in to the OS instead of being a separate program. Although it kind of depends on how it works in Tiger, but I assume there'll be a way to do it without having some app-looking item left open afterward.
I don't launch iSync when I sync data. I just use the sync menu and trigger it from there. If I ever want to view the sync log or there are conflicts, then and only then do I use the main iSync app.
But if the iSync opened without me directly launching it, it should quit once the sync is done.
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Theoretically if you just wait until Tiger comes out then that problem will be null and void.
But if the iSync opened without me directly launching it, it should quit once the sync is done.