This method 100% guarantees all pins will align when reassembled.
Here is how to avoid the issue:
Glue or clamp one scale to the tang.
Drill the holes from the tang side, placing pins through the holes as you go.
Remove the pins and clamp/glue the other scale on.
Drilling from the already drilled side, drill through the second scale, placing the pins in the holes as you drill.
Other tips -
Drill the tang holes 15-25% oversize. This prevents binding when inserting the pins.
Use sharp and short drill bits.
The pins should slip through smoothly, not tight, not loose. Select the right size bit and use a reamer if necessary.