I like bimr's idea provided it's allowable from a code standpoint.
As I understand it, he is suggesting wiring the output for pump control to a receptacle (GFCI) external to the control panel. The pump, instead of being wired directly into the control panel, would instead terminate in a standard 3 prong plug. In the event of a power outage, the pump could be unplugged from the receptacle and plugged directly into the generator, bypassing the controls.
Alternatively, the entire control panel could be connected in that fashion. Instead of the panel being hardwired into the house, it could be supplied with power via a plug and receptacle.
In either situation though, I worry that the plug/receptacle would have to be secured in some fashion to prevent tampering. Want to get back at your neighbor? Unplug his pump/controls. Although with bimr's idea you'd still get a high water alarm in the event someone disconnected the pump.
Let us know what you decide and are able to get approved.