[Ed Zachary]

What?

I am an Alltel-to-Verizon customer as well.
Never had to do anything untoward to use GPS. Before or after the merger. I just downloaded and installed Google Maps, turned on GPS in the phone's settings (services|location), and turned on Use GPS in Google Maps.
I believe it was Verizon that locked GPS on their phones, not Alltel.

The merger, like nearly all mergers, entailed the acquired company's accounts becoming the property of the acquirer. So the accounts got "moved" to Verizon be virtue of being part of the property being sold.

Equipment was also a part of the deal, so all the Alltel equipment, except of course, the parts that were divested after the merger, is part of the merge of the two systems.
The merger of equipment obviously could not happen overnight. That would be a physical impossibility. Rather, that merger is an ongoing process. An Alltel-cum-Verizon customer does not need to do anything with the phone like flashing, upgrading, or otherwise diddling with the software in order for it to work on the Verizon network.