The serial port can only supply a small current, certainly not enough to power a laser pointer, so you're still going to have to use the batteries...
Find the negative power supply in your laser pointer (the - that comes from the batteriers), cut this wire and connect it to the 'battery -' on the scematic. The 'Laser -' exit should then be connected to the other end...
about the software, is there any chanse you have visual basic? it whould be very simple to in VB...
if it really has to be C, then for wich platform? dos, windows ?