A classic trick to avoid Emacs pinky is swapping Caps Lock and Ctrl. I'm using it everywhere though; swapcaps makes it much more comfortable to use the Ctrl key on a standard PC keyboard.
Truly hardcore modifier wizards (or people recovering from injury) have been known to use pedals.
Ideal would be to use a keyboard and OS (MacBooks have both) where you can map Control to the keys immediately next to the spacebar. Using the strongest finger (thumb) instead of the weakest finger and the strongest movement (thumb curl) rather than the weakest is a true upgrade.
On every keyboard I have in my apartment, and every keyboard I've used for a long time, moving my left pinky straight down with my hands on the home row hits left shift and the windows key, in that order. Hitting caps lock with my left pinky is barely a movement at all.