I'm with Tony on the rebuild, but mostly because I prefer the look of the ATE caliper, and I like to save good parts.
Furthermore, though I don't have experience with both, but I'm willing to bet the ATE caliper finish is more resilient. I had to weld a big grade 8 nut onto one of my caliper bolts (that hold the caliper together) to remove it. The heat didn't bother a thing on the ATE. Not sure if the black painted Brembos would fare as well.
You could also consider re-chroming the ATE pistons.
IIRC, you have the holes for calipers on both fork sliders. If you are considering going to a dual disc setup, you might consider that in deciding your brand of caliper as well.
@Tony
1) I think the ATE and Brembo pads have a different shape on the backing plate. I'm pretty sure the ears on the pad are different to accommodate different anti-rattle springs. Julio A. has a thread on this in the FAQ section. The R65 Brembo/ATE calipers are each unique to the R65. Are you confusing them with the calipers on the big brothers?
2) Your post on turning new pistons was my inspiration to do the same when the need arises
3) While I have broken the rules with what is "acceptable" on vehicular repair, I find that it is best left to the person with wrench in hand to determine what will fly. If in question, listen to the cautious voice. Though your friend might have laughed at you for replacing your cruddy pistons, a clean set of pistons could prolong the life of a new piston seals. Some folks aren't willing to chance the fact that a rough piston could prematurely wear through a seal and lead to a sudden failure of the braking system.