KAITAI
I think you misunderstood what I said, I didn't mean that they were screwed in, - I meant that you could machine them down flush with the aluminium, using a lathe (turning), or milling them down using a milling machine.
The part of the pin still left in the flywheel would be ok remaining there.

If you haven't got access to these machines, you could possibly hacksaw the pins off, and file them flush.

The other method is, (I do think Mike's idea would work too), drilling from the back, - however, if you're drilling from the back, use a drill a little smaller dia. than that of the pin, and just drill in as far as necessary (ie the depth of the aluminium), don't drill right through the pin. This will leave a thin wall steel tube in the al. with a solid core to hit with the punch and will then be easy to drive out.
As Mike says, use a pilot drill first, and try to get it central.

Bashing flywheels I don't like, unless the pins come out first or second thump.