This qualifies under category circuit rework.
The "best" solution, if the pads are still usable, is to purchase the replacement part and re-attach it. The part is about $1 USD but this does not include shipping Vendor Link (Part Number Found in Schematic)
It is generally a good idea to repair something to its original state. Most things can be repaired if desired, for example, the guides I reference below also have sections for repairing traces inside boards. Where there is a will (or an irreplaceable part) there is, usually, a way. An, in fact, there are companies you can pay to do this.
Rework is not trivial, for reattaching the original component you should follow rework procedures for leaded surface mount components, a good guide is available here
Figure: Illustration representing soldering a leaded component
There are also guides for repairing the missing metal pads, but this is not easy.
What is critical for reattaching connectors is that the heavy duty metal tabs can be soldered down, if that pad is gone you will never have mechanical stability. However, setting it with epoxy can be a substitute
If you do not wish to mount a replacement part, then you should use wire jumpers to create leads for you to attach your power supply to.
The critical thing with using wire jumpers on surface mount pads is to eliminate the possibility of any "pulling" on the wire, no matter what happens at the business end, this is known as Strain Relief
For a good guide on using wire jumpers see this guide
Attach those wires to the two outside pads of the connector footprint.
If those pads are destroyed, there are solderable test pads (aka Probe Points) on the board, indicated on the schematic as
PP6 which are connected to the USB side of the power supply. You may use these instead of the pads directly on the USB footprint.
Figure: Schematic Portion showing USB Connector and connected Probe Points (Raspberry Pi 3)
Figure: Board Section where the relevant probe points are found (Back of Board - Raspberry Pi 3)
1. Use existing holes for strain relief
Figure: Routing a jumper through a via for strain relief
2. Route the wire flush to the board add extra "wiggles" to the wire as a form of mechanical strain relief.
Figure: Example of Routing a Jumper Wire along the surface of a PCB
Kapton Tape (polyimide film tape) to secure the wire to the board, leave dangling ends
Figure: I have nothing but good things to say about this tape, the best tape for electronics work, temperature safe to 250C
4. Either solder the jumper wires directly to your power supply, modify a usb extension cable or use a screw terminal breakout board to create a place to connect a standard USB power Supply
Figure: This is one example of a screw terminal breakout board, there are many many others