Unfortunately, I'd bet that separation of Legion/Ambuscade would be impossible. Ambuscade was designed to operate inside Legion zone, so changing that would be tantamount to rewriting the event system itself. Given the amount of dev resistance to simple adjustments to the reward menu/system, I rather doubt there'd be any hope of an even larger change..

Reservation of 1-2 Legion instances for the event itself though should be quite possible and less complex to implement than changing Legion to utilize the entry queue. Demand for entry into Legion is not super high, so even with only a single instance reserved, at worst you'd have to wait until those inside got out if it was busy. As it is, during the first 2-3 weeks of each Ambuscade cycle it's very close to impossible to get into Legion even if you are the only player who wants to get in.