In a tournament last weekend, one of the players on my card walked up to his mini marker (after marking his throw) with two different putters. While standing at his marker, he decided which putter to use and threw the other (from his marker) over to his bag which was about 6-7 feet away.

I know he wasn't trying to make the putt by tossing aside his other putter, but would or could he be stroked for that?

If it was away from the basket, 6ft is less than 2m. No penalty.

6ft and not toward the target apply to practice throws.
Practice throws are throws made from anywhere on the course that is not your lie.
Real throws are throws of any distance in any direction made from a live lie.

The first propulsion of a disc from a live lie counts as the players competitive throw, even if it is backwards towards their bag. Always discard the discs you do not want before you step to your lie, or from off the tee pad.