Much Smaller Wafers and Much Larger Chips
Smaller wafers require smaller foundries, which should be more survivable. This will drive the foundries to older tech, so the transistors will be larger.
Process
In a nutshell, chip manufacturing is "Build a siliconesilicon wafer, put the wafer through a bunch of highly specialized machinery."
All this machinery must exist in a clean room, because static, dust, etc. will damage the end product. The high cost of building a foundry is partly a function of the high precision of those machines, and partly a function of building and maintaining a clean room.
The Change
So instead of starting with a wafer the size of a serving plate (12 inch diameter) go back to the "good old days" of the 1960s, and start with a 1 inch diameter wafer.
Now you get to scale down all of the other equipment!
The size of your clean room should go way down, which should make it much cheaper to build and maintain. Thus the investment is less, and the destruction of your factory is less catastrophic.
A smaller foundry should also be easier to protect - it's easier to bury, easier to monitor the perimeter, etc.
But won't you need more Foundries?
Yes.
But that's OK - instead of building a few, very expensive photoliography setups, you build lots of cheap ones. Build factories to build your chip factories.
Sure, you won't be able to keep the quality up - that's why you go with larger transistors, because the precision requirements are lower.
End Result
You'd probably end up with more expensive, less powerful chips, but you could have dozens of foundries spread across the country, each one churning out a relatively low volume of product.