It's a water pump, right? So the worst thing that will happen is that it
will leak coolant. No big deal. So I would just bolt it up with the
remaining bolts and a big gob of RTV gasket goop and see if it leaks...

Unless you want to pull the motor, you aren't going to be able to either
drill it straight, keep nitric acid on it, or any of the other solutions...

BTW, my 19 year-old smart-alek son calls this 'Hardy boy' work, as in, "Dad,
you going to Hardy boy this thing or do it right?"