Wind can certainly do nasty things, but like you said, at only 100 yards it shouldn't be that bad, assuming that you are shooting from a steady rest. Bullet weight makes a difference also. I like the 140 grain bullets best, but the 129 and 120 grain bullets are fine for deer. They may blow around a bit more than the 140s do, but the 6.5 mm bullets are long, skinny and stable as heck.
Whenever I mount (or remount) a scope I boresight it. There are often adjustments one can make with the scope mounts that get things reasonably centered before you start clicking the scope adjustments. It is best if you can start out with the scope adjustments centered so that you have the maximum adjustment either way available to you once the screws are all buttoned down.
Anyway, if your shots are at or under 100 yards, a three inch offset may not be the end of the world, since deer have an 8" to 10" kill spot. I would sure feel more comfortable if I could find a place to do a bit more shooting though before taking shots at game, if for no other reason that to feel more confident.
Good luck, and GREAT choice of rifle and caliber!