I'm not sure if I can help with the bigger picture or not, but we have a product (RouteWriter) which helps with the pushpins <-> MapPoint routes side of things, rather than the Excel Import side of things.
RouteWriter writes the pushpins to Excel in route order - ie. you've created your route, and you just want the order of the pins (and the other pin data).
RouteWriter includes RouteReader which can create a route from existing pushpins, inserting the pins in a pre-defined order. The order is set using a data field (eg. a sequence number). Note that manually importing pins (as above) does not allow you to add custom data fields - you have to use one of MapPoint's wizards; but this probably academic because if you're adding the pins programmatically, you can also insert them in any order you feel like.
RouteWriter: Export Routes from Microsoft MapPoint
Richard