3 options:
1 - cheapest option, and easiest. Drill out the holes so you can re-tap them for 7/16-14 or 1/2-13 threads, drill out the holes in your crank pulley, and bolt it all back together with bigger bolts...then you don't have to change or pull the balancer. A tap and 3 bolts is cheaper than a balancer
2 - drill and tap the holes oversize as in option one, and use different bolts with your puller to get the balancer off.
3 - if it's an OE type balancer, there is 3 windows in it and the hub is only about 1/2" thick. You should be able to use 3/8 bolts and sneek your fingers through the windows in the balancer to get some nuts on the bolts...then use your puller like you normally would.
I like option one.