Being in a scrimmage kick formation has nothing to do with running into or roughing the kicker, so we can discount that element. And, just because the snapped ball touched the ground, that does not change anything about running into/roughing the kicker rules. So, we can discount that, too.
The only criterion, then, is the judgment as to whether or not it was obvious a scrimmage kick would be made (not 'might' be made, but 'would' be made). If you think it was still obvious he would make a kick, then you should have thrown a flag. But, if you don't think it was obvious, then no foul.
By what you describe, like Osric, it sounds as though it was initially obvious, and he didn't do anything to make it seem otherwise. Since he was able to recover the ball, and immediately get into a kicking motion, it sounds like it was still obvious he was going to kick the ball. Assuming he made no side-step, or any hesitation after recovering the ball, I'd say he had protection, and roughing should have been called. But, that's based on writtten description. I might change my mind completely, if I saw some good video.