Could modern military aircraft be retrofitted to work with alternative fuels instead of kerosene?
Petroleum isn't going to be finished for a very long time. We keep discovering and accepting trickier, dirtier, and/or costlier ways to get more oil - shale is just the last step in a long chain. 

Yes, planes could be altered to use other fuels such as biodiesel. It has been done. This will require changes to the fuel system, to handle such considerably more contaminated fuel, increased fuel heating, possibly combustor alterations.

However, on a practical basis, it only makes sense to start replacing aviation fuels en masse once most road vehicles have switched to a different fuel. Aviation is weight-critical and an energy-dense fuel matters; it's also a smaller consumer than road vehicles. Also, aviation's safety and maintenance requirements call for cleaner and more consistent fuels than acceptable on the road. 

For the military, fuel consumption and costs have traditionally been considered less important. It's going to get the fuel its jets need, since there will be plenty available for the foreseeable future.